Commit 986c7424 authored by Jake Freimer's avatar Jake Freimer
Browse files

Add paper RNA-Seq and ATAC-Seq pipelines

parent 9587527e

.gitignore

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.Rhistory



.DS_Store

ATAC_Seq_pipeline/ATAC_samplesheet.txt

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Original line number Diff line number Diff line 
Name	Read1_1	Read2_1

Donor_1_AAVS1_1_C3	JFAM15/Donor_1_AAVS1_1_C3_S42_L002_R1_001.fastq.gz	JFAM15/Donor_1_AAVS1_1_C3_S42_L002_R2_001.fastq.gz

Donor_1_AAVS1_2_A3	JFAM15/Donor_1_AAVS1_2_A3_S18_L002_R1_001.fastq.gz	JFAM15/Donor_1_AAVS1_2_A3_S18_L002_R2_001.fastq.gz

Donor_1_AAVS1_3_B10	JFAM15/Donor_1_AAVS1_3_B10_S37_L002_R1_001.fastq.gz	JFAM15/Donor_1_AAVS1_3_B10_S37_L002_R2_001.fastq.gz

Donor_1_AAVS1_4_A1	JFAM15/Donor_1_AAVS1_4_A1_S16_L002_R1_001.fastq.gz	JFAM15/Donor_1_AAVS1_4_A1_S16_L002_R2_001.fastq.gz

Donor_1_AAVS1_5_B7	JFAM15/Donor_1_AAVS1_5_B7_S34_L002_R1_001.fastq.gz	JFAM15/Donor_1_AAVS1_5_B7_S34_L002_R2_001.fastq.gz

Donor_1_AAVS1_6_B4	JFAM15/Donor_1_AAVS1_6_B4_S31_L002_R1_001.fastq.gz	JFAM15/Donor_1_AAVS1_6_B4_S31_L002_R2_001.fastq.gz

Donor_1_AAVS1_7_A11	JFAM15/Donor_1_AAVS1_7_A11_S26_L002_R1_001.fastq.gz	JFAM15/Donor_1_AAVS1_7_A11_S26_L002_R2_001.fastq.gz

Donor_1_AAVS1_8_A9	JFAM15/Donor_1_AAVS1_8_A9_S24_L002_R1_001.fastq.gz	JFAM15/Donor_1_AAVS1_8_A9_S24_L002_R2_001.fastq.gz

Donor_1_ATXN7L3_C5	JFAM15/Donor_1_ATXN7L3_C5_S44_L002_R1_001.fastq.gz	JFAM15/Donor_1_ATXN7L3_C5_S44_L002_R2_001.fastq.gz

Donor_1_CBFB_C8	JFAM15/Donor_1_CBFB_C8_S47_L002_R1_001.fastq.gz	JFAM15/Donor_1_CBFB_C8_S47_L002_R2_001.fastq.gz

Donor_1_ETS1_C6	JFAM15/Donor_1_ETS1_C6_S45_L002_R1_001.fastq.gz	JFAM15/Donor_1_ETS1_C6_S45_L002_R2_001.fastq.gz

Donor_1_FOXK1_A8	JFAM15/Donor_1_FOXK1_A8_S23_L002_R1_001.fastq.gz	JFAM15/Donor_1_FOXK1_A8_S23_L002_R2_001.fastq.gz

Donor_1_FOXP1_B8	JFAM15/Donor_1_FOXP1_B8_S35_L002_R1_001.fastq.gz	JFAM15/Donor_1_FOXP1_B8_S35_L002_R2_001.fastq.gz

Donor_1_GATA3_A5	JFAM15/Donor_1_GATA3_A5_S20_L002_R1_001.fastq.gz	JFAM15/Donor_1_GATA3_A5_S20_L002_R2_001.fastq.gz

Donor_1_HIVEP2_B5	JFAM15/Donor_1_HIVEP2_B5_S32_L002_R1_001.fastq.gz	JFAM15/Donor_1_HIVEP2_B5_S32_L002_R2_001.fastq.gz

Donor_1_IL2RA_B9	JFAM15/Donor_1_IL2RA_B9_S36_L002_R1_001.fastq.gz	JFAM15/Donor_1_IL2RA_B9_S36_L002_R2_001.fastq.gz

Donor_1_IRF1_B12	JFAM15/Donor_1_IRF1_B12_S39_L002_R1_001.fastq.gz	JFAM15/Donor_1_IRF1_B12_S39_L002_R2_001.fastq.gz

Donor_1_IRF2_B6	JFAM15/Donor_1_IRF2_B6_S33_L002_R1_001.fastq.gz	JFAM15/Donor_1_IRF2_B6_S33_L002_R2_001.fastq.gz

Donor_1_IRF4_C7	JFAM15/Donor_1_IRF4_C7_S46_L002_R1_001.fastq.gz	JFAM15/Donor_1_IRF4_C7_S46_L002_R2_001.fastq.gz

Donor_1_JAK3_B11	JFAM15/Donor_1_JAK3_B11_S38_L002_R1_001.fastq.gz	JFAM15/Donor_1_JAK3_B11_S38_L002_R2_001.fastq.gz

Donor_1_KLF2_A4	JFAM15/Donor_1_KLF2_A4_S19_L002_R1_001.fastq.gz	JFAM15/Donor_1_KLF2_A4_S19_L002_R2_001.fastq.gz

Donor_1_KMT2A_C2	JFAM15/Donor_1_KMT2A_C2_S41_L002_R1_001.fastq.gz	JFAM15/Donor_1_KMT2A_C2_S41_L002_R2_001.fastq.gz

Donor_1_MBD2_C4	JFAM15/Donor_1_MBD2_C4_S43_L002_R1_001.fastq.gz	JFAM15/Donor_1_MBD2_C4_S43_L002_R2_001.fastq.gz

Donor_1_MED12_C1	JFAM15/Donor_1_MED12_C1_S40_L002_R1_001.fastq.gz	JFAM15/Donor_1_MED12_C1_S40_L002_R2_001.fastq.gz

Donor_1_MYB_B1	JFAM15/Donor_1_MYB_B1_S28_L002_R1_001.fastq.gz	JFAM15/Donor_1_MYB_B1_S28_L002_R2_001.fastq.gz

Donor_1_RELA_A2	JFAM15/Donor_1_RELA_A2_S17_L002_R1_001.fastq.gz	JFAM15/Donor_1_RELA_A2_S17_L002_R2_001.fastq.gz

Donor_1_STAT5A_B3	JFAM15/Donor_1_STAT5A_B3_S30_L002_R1_001.fastq.gz	JFAM15/Donor_1_STAT5A_B3_S30_L002_R2_001.fastq.gz

Donor_1_STAT5B_A10	JFAM15/Donor_1_STAT5B_A10_S25_L002_R1_001.fastq.gz	JFAM15/Donor_1_STAT5B_A10_S25_L002_R2_001.fastq.gz

Donor_1_TNFAIP3_A12	JFAM15/Donor_1_TNFAIP3_A12_S27_L002_R1_001.fastq.gz	JFAM15/Donor_1_TNFAIP3_A12_S27_L002_R2_001.fastq.gz

Donor_1_YY1_B2	JFAM15/Donor_1_YY1_B2_S29_L002_R1_001.fastq.gz	JFAM15/Donor_1_YY1_B2_S29_L002_R2_001.fastq.gz

Donor_1_ZNF217_A6	JFAM15/Donor_1_ZNF217_A6_S21_L002_R1_001.fastq.gz	JFAM15/Donor_1_ZNF217_A6_S21_L002_R2_001.fastq.gz

Donor_3_AAVS1_1_E11	JFAM15/Donor_3_AAVS1_1_E11_S74_L002_R1_001.fastq.gz	JFAM15/Donor_3_AAVS1_1_E11_S74_L002_R2_001.fastq.gz

Donor_3_AAVS1_2_C11	JFAM15/Donor_3_AAVS1_2_C11_S50_L002_R1_001.fastq.gz	JFAM15/Donor_3_AAVS1_2_C11_S50_L002_R2_001.fastq.gz

Donor_3_AAVS1_3_E6	JFAM15/Donor_3_AAVS1_3_E6_S69_L002_R1_001.fastq.gz	JFAM15/Donor_3_AAVS1_3_E6_S69_L002_R2_001.fastq.gz

Donor_3_AAVS1_5_E3	JFAM15/Donor_3_AAVS1_5_E3_S66_L002_R1_001.fastq.gz	JFAM15/Donor_3_AAVS1_5_E3_S66_L002_R2_001.fastq.gz

Donor_3_AAVS1_6_D12	JFAM15/Donor_3_AAVS1_6_D12_S63_L002_R1_001.fastq.gz	JFAM15/Donor_3_AAVS1_6_D12_S63_L002_R2_001.fastq.gz

Donor_3_AAVS1_7_D7	JFAM15/Donor_3_AAVS1_7_D7_S58_L002_R1_001.fastq.gz	JFAM15/Donor_3_AAVS1_7_D7_S58_L002_R2_001.fastq.gz

Donor_3_AAVS1_8_D5	JFAM15/Donor_3_AAVS1_8_D5_S56_L002_R1_001.fastq.gz	JFAM15/Donor_3_AAVS1_8_D5_S56_L002_R2_001.fastq.gz

Donor_3_ATXN7L3_F1	JFAM15/Donor_3_ATXN7L3_F1_S76_L002_R1_001.fastq.gz	JFAM15/Donor_3_ATXN7L3_F1_S76_L002_R2_001.fastq.gz

Donor_3_CBFB_F4	JFAM15/Donor_3_CBFB_F4_S79_L002_R1_001.fastq.gz	JFAM15/Donor_3_CBFB_F4_S79_L002_R2_001.fastq.gz

Donor_3_ETS1_F2	JFAM15/Donor_3_ETS1_F2_S77_L002_R1_001.fastq.gz	JFAM15/Donor_3_ETS1_F2_S77_L002_R2_001.fastq.gz

Donor_3_FOXK1_D4	JFAM15/Donor_3_FOXK1_D4_S55_L002_R1_001.fastq.gz	JFAM15/Donor_3_FOXK1_D4_S55_L002_R2_001.fastq.gz

Donor_3_FOXP1_E4	JFAM15/Donor_3_FOXP1_E4_S67_L002_R1_001.fastq.gz	JFAM15/Donor_3_FOXP1_E4_S67_L002_R2_001.fastq.gz

Donor_3_GATA3_D1	JFAM15/Donor_3_GATA3_D1_S52_L002_R1_001.fastq.gz	JFAM15/Donor_3_GATA3_D1_S52_L002_R2_001.fastq.gz

Donor_3_HIVEP2_E1	JFAM15/Donor_3_HIVEP2_E1_S64_L002_R1_001.fastq.gz	JFAM15/Donor_3_HIVEP2_E1_S64_L002_R2_001.fastq.gz

Donor_3_IL2RA_E5	JFAM15/Donor_3_IL2RA_E5_S68_L002_R1_001.fastq.gz	JFAM15/Donor_3_IL2RA_E5_S68_L002_R2_001.fastq.gz

Donor_3_IRF1_E8	JFAM15/Donor_3_IRF1_E8_S71_L002_R1_001.fastq.gz	JFAM15/Donor_3_IRF1_E8_S71_L002_R2_001.fastq.gz

Donor_3_IRF2_E2	JFAM15/Donor_3_IRF2_E2_S65_L002_R1_001.fastq.gz	JFAM15/Donor_3_IRF2_E2_S65_L002_R2_001.fastq.gz

Donor_3_IRF4_F3	JFAM15/Donor_3_IRF4_F3_S78_L002_R1_001.fastq.gz	JFAM15/Donor_3_IRF4_F3_S78_L002_R2_001.fastq.gz

Donor_3_JAK3_E7	JFAM15/Donor_3_JAK3_E7_S70_L002_R1_001.fastq.gz	JFAM15/Donor_3_JAK3_E7_S70_L002_R2_001.fastq.gz

Donor_3_KLF2_C12	JFAM15/Donor_3_KLF2_C12_S51_L002_R1_001.fastq.gz	JFAM15/Donor_3_KLF2_C12_S51_L002_R2_001.fastq.gz

Donor_3_KMT2A_E10	JFAM15/Donor_3_KMT2A_E10_S73_L002_R1_001.fastq.gz	JFAM15/Donor_3_KMT2A_E10_S73_L002_R2_001.fastq.gz

Donor_3_MBD2_E12	JFAM15/Donor_3_MBD2_E12_S75_L002_R1_001.fastq.gz	JFAM15/Donor_3_MBD2_E12_S75_L002_R2_001.fastq.gz

Donor_3_MED12_E9	JFAM15/Donor_3_MED12_E9_S72_L002_R1_001.fastq.gz	JFAM15/Donor_3_MED12_E9_S72_L002_R2_001.fastq.gz

Donor_3_MYB_D9	JFAM15/Donor_3_MYB_D9_S60_L002_R1_001.fastq.gz	JFAM15/Donor_3_MYB_D9_S60_L002_R2_001.fastq.gz

Donor_3_PTEN_D3	JFAM15/Donor_3_PTEN_D3_S54_L002_R1_001.fastq.gz	JFAM15/Donor_3_PTEN_D3_S54_L002_R2_001.fastq.gz

Donor_3_RELA_C10	JFAM15/Donor_3_RELA_C10_S49_L002_R1_001.fastq.gz	JFAM15/Donor_3_RELA_C10_S49_L002_R2_001.fastq.gz

Donor_3_STAT5A_D11	JFAM15/Donor_3_STAT5A_D11_S62_L002_R1_001.fastq.gz	JFAM15/Donor_3_STAT5A_D11_S62_L002_R2_001.fastq.gz

Donor_3_TNFAIP3_D8	JFAM15/Donor_3_TNFAIP3_D8_S59_L002_R1_001.fastq.gz	JFAM15/Donor_3_TNFAIP3_D8_S59_L002_R2_001.fastq.gz

Donor_3_YY1_D10	JFAM15/Donor_3_YY1_D10_S61_L002_R1_001.fastq.gz	JFAM15/Donor_3_YY1_D10_S61_L002_R2_001.fastq.gz

Donor_3_ZNF217_D2	JFAM15/Donor_3_ZNF217_D2_S53_L002_R1_001.fastq.gz	JFAM15/Donor_3_ZNF217_D2_S53_L002_R2_001.fastq.gz

Donor_4_AAVS1_1_H7	JFAM15/Donor_4_AAVS1_1_H7_S106_L002_R1_001.fastq.gz	JFAM15/Donor_4_AAVS1_1_H7_S106_L002_R2_001.fastq.gz

Donor_4_AAVS1_2_F7	JFAM15/Donor_4_AAVS1_2_F7_S82_L002_R1_001.fastq.gz	JFAM15/Donor_4_AAVS1_2_F7_S82_L002_R2_001.fastq.gz

Donor_4_AAVS1_3_H2	JFAM15/Donor_4_AAVS1_3_H2_S101_L002_R1_001.fastq.gz	JFAM15/Donor_4_AAVS1_3_H2_S101_L002_R2_001.fastq.gz

Donor_4_AAVS1_4_F5	JFAM15/Donor_4_AAVS1_4_F5_S80_L002_R1_001.fastq.gz	JFAM15/Donor_4_AAVS1_4_F5_S80_L002_R2_001.fastq.gz

Donor_4_AAVS1_5_G11	JFAM15/Donor_4_AAVS1_5_G11_S98_L002_R1_001.fastq.gz	JFAM15/Donor_4_AAVS1_5_G11_S98_L002_R2_001.fastq.gz

Donor_4_AAVS1_6_G8	JFAM15/Donor_4_AAVS1_6_G8_S95_L002_R1_001.fastq.gz	JFAM15/Donor_4_AAVS1_6_G8_S95_L002_R2_001.fastq.gz

Donor_4_AAVS1_7_G3	JFAM15/Donor_4_AAVS1_7_G3_S90_L002_R1_001.fastq.gz	JFAM15/Donor_4_AAVS1_7_G3_S90_L002_R2_001.fastq.gz

Donor_4_AAVS1_8_G1	JFAM15/Donor_4_AAVS1_8_G1_S88_L002_R1_001.fastq.gz	JFAM15/Donor_4_AAVS1_8_G1_S88_L002_R2_001.fastq.gz

Donor_4_ATXN7L3_H9	JFAM15/Donor_4_ATXN7L3_H9_S108_L002_R1_001.fastq.gz	JFAM15/Donor_4_ATXN7L3_H9_S108_L002_R2_001.fastq.gz

Donor_4_CBFB_H12	JFAM15/Donor_4_CBFB_H12_S111_L002_R1_001.fastq.gz	JFAM15/Donor_4_CBFB_H12_S111_L002_R2_001.fastq.gz

Donor_4_ETS1_H10	JFAM15/Donor_4_ETS1_H10_S109_L002_R1_001.fastq.gz	JFAM15/Donor_4_ETS1_H10_S109_L002_R2_001.fastq.gz

Donor_4_FOXK1_F12	JFAM15/Donor_4_FOXK1_F12_S87_L002_R1_001.fastq.gz	JFAM15/Donor_4_FOXK1_F12_S87_L002_R2_001.fastq.gz

Donor_4_FOXP1_G12	JFAM15/Donor_4_FOXP1_G12_S99_L002_R1_001.fastq.gz	JFAM15/Donor_4_FOXP1_G12_S99_L002_R2_001.fastq.gz

Donor_4_GATA3_F9	JFAM15/Donor_4_GATA3_F9_S84_L002_R1_001.fastq.gz	JFAM15/Donor_4_GATA3_F9_S84_L002_R2_001.fastq.gz

Donor_4_HIVEP2_G9	JFAM15/Donor_4_HIVEP2_G9_S96_L002_R1_001.fastq.gz	JFAM15/Donor_4_HIVEP2_G9_S96_L002_R2_001.fastq.gz

Donor_4_IL2RA_H1	JFAM15/Donor_4_IL2RA_H1_S100_L002_R1_001.fastq.gz	JFAM15/Donor_4_IL2RA_H1_S100_L002_R2_001.fastq.gz

Donor_4_IRF1_H4	JFAM15/Donor_4_IRF1_H4_S103_L002_R1_001.fastq.gz	JFAM15/Donor_4_IRF1_H4_S103_L002_R2_001.fastq.gz

Donor_4_IRF2_G10	JFAM15/Donor_4_IRF2_G10_S97_L002_R1_001.fastq.gz	JFAM15/Donor_4_IRF2_G10_S97_L002_R2_001.fastq.gz

Donor_4_IRF4_H11	JFAM15/Donor_4_IRF4_H11_S110_L002_R1_001.fastq.gz	JFAM15/Donor_4_IRF4_H11_S110_L002_R2_001.fastq.gz

Donor_4_JAK3_H3	JFAM15/Donor_4_JAK3_H3_S102_L002_R1_001.fastq.gz	JFAM15/Donor_4_JAK3_H3_S102_L002_R2_001.fastq.gz

Donor_4_KLF2_F8	JFAM15/Donor_4_KLF2_F8_S83_L002_R1_001.fastq.gz	JFAM15/Donor_4_KLF2_F8_S83_L002_R2_001.fastq.gz

Donor_4_KMT2A_H6	JFAM15/Donor_4_KMT2A_H6_S105_L002_R1_001.fastq.gz	JFAM15/Donor_4_KMT2A_H6_S105_L002_R2_001.fastq.gz

Donor_4_MBD2_H8	JFAM15/Donor_4_MBD2_H8_S107_L002_R1_001.fastq.gz	JFAM15/Donor_4_MBD2_H8_S107_L002_R2_001.fastq.gz

Donor_4_MED12_H5	JFAM15/Donor_4_MED12_H5_S104_L002_R1_001.fastq.gz	JFAM15/Donor_4_MED12_H5_S104_L002_R2_001.fastq.gz

Donor_4_MYB_G5	JFAM15/Donor_4_MYB_G5_S92_L002_R1_001.fastq.gz	JFAM15/Donor_4_MYB_G5_S92_L002_R2_001.fastq.gz

Donor_4_PTEN_F11	JFAM15/Donor_4_PTEN_F11_S86_L002_R1_001.fastq.gz	JFAM15/Donor_4_PTEN_F11_S86_L002_R2_001.fastq.gz

Donor_4_RELA_F6	JFAM15/Donor_4_RELA_F6_S81_L002_R1_001.fastq.gz	JFAM15/Donor_4_RELA_F6_S81_L002_R2_001.fastq.gz

Donor_4_STAT5A_G7	JFAM15/Donor_4_STAT5A_G7_S94_L002_R1_001.fastq.gz	JFAM15/Donor_4_STAT5A_G7_S94_L002_R2_001.fastq.gz

Donor_4_STAT5B_G2	JFAM15/Donor_4_STAT5B_G2_S89_L002_R1_001.fastq.gz	JFAM15/Donor_4_STAT5B_G2_S89_L002_R2_001.fastq.gz

Donor_4_TNFAIP3_G4	JFAM15/Donor_4_TNFAIP3_G4_S91_L002_R1_001.fastq.gz	JFAM15/Donor_4_TNFAIP3_G4_S91_L002_R2_001.fastq.gz

Donor_4_YY1_G6	JFAM15/Donor_4_YY1_G6_S93_L002_R1_001.fastq.gz	JFAM15/Donor_4_YY1_G6_S93_L002_R2_001.fastq.gz

Donor_4_ZNF217_F10	JFAM15/Donor_4_ZNF217_F10_S85_L002_R1_001.fastq.gz	JFAM15/Donor_4_ZNF217_F10_S85_L002_R2_001.fastq.gz
 
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ATAC_Seq_pipeline/Snakefile

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ATAC_Seq_pipeline/analysis/differential_peaks.R

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library('tidyverse')

library("vroom")

library("DESeq2")

library('edgeR')



# ------------------------------------------------------------------------------------------------

# TSS enrichment scores as surrogate for sample quality

enrichment_files <- dir("~/Google_Drive/Research/analysis_data/tf_screens/atac/il2ra_hits/tss", full.names = T, pattern = ".csv")



enrichment_df <- lapply(enrichment_files, function(x) {

  read_csv(x)

}) %>%

  bind_rows() %>%

  mutate(Sample = gsub("_[A-Z][0-9]{0,2}$", "", Sample))



# Function to run DESeq2 on each sample

run_deseq2_tss_unscaled <- function(gene_ko, count_df) {

  

  # Select relevant samples and generate count matrix

  count_mat <- as.matrix(dplyr::select(count_df, matches(paste0("AAVS1|", gene_ko))))

  

  # Filter low count reads

  min_cpm <- ceiling(10 / (min(colSums(count_mat)) / 1e6))

  count_mat_filtered <- count_mat[rowSums(cpm(count_mat) > min_cpm) >= 3, ]

  print(dim(count_mat_filtered))

  

  # Pull out just sample names and set up design matrix

  layout <- data.frame(sample = colnames(count_mat_filtered)) %>%

    mutate(

      ko = gsub("Donor_[0-9]_", "", sample),

      ko = gsub("AAVS1_[0-9]", "AAVS1", ko),

      donor = str_extract(sample, "Donor_[0-9]")

    ) %>%

    inner_join(., enrichment_df, by = c("sample" = "Sample"))

  

  print(layout)

  

  # Run DESeq2

  dds <- DESeqDataSetFromMatrix(

    countData = count_mat_filtered,

    colData = layout,

    design = ~ max_tss_enrichment + donor + ko

  )

  

  dds <- DESeq(dds)

  res <- results(dds, c("ko", gene_ko, "AAVS1"))

  resDF <- as.data.frame(res) %>%

    mutate(

      sample = gene_ko,

      peakName = rownames(res)

    )

}





# read in counts

counts <- vroom('~/Google_Drive/Research/analysis_data/tf_screens/atac/il2ra_hits/counts/count_mat_peaks_cluster150bp_peak_size_350bp.txt')



counts <- as.data.frame(counts)



rownames(counts) <- counts$name



# remove well position

colnames(counts) <- gsub("_[A-Z][0-9]{0,2}$", "", colnames(counts))



# Extract samples from count dataframe

samples <- unique(str_subset(gsub("Donor_[0-9]_", "", str_subset(colnames(counts), "Donor")), "AAVS1", negate = TRUE))



# Run deseq2 

deseq2_results <- lapply(samples, function(x) run_deseq2_tss_unscaled(x, counts))



write_rds(deseq2_results, paste0('~/Google_Drive/Research/analysis_data/tf_screens/atac/il2ra_hits/analysis_data/differential_peaks_deseq2_', Sys.Date(), '.RDS'))

ATAC_Seq_pipeline/envs/atac_seq.yaml

0 → 100644
+17 −0
Original line number Diff line number Diff line 
channels:

  - conda-forge

  - bioconda

  - defaults

dependencies:

  - cutadapt=2.10

  - bowtie2=2.4.1

  - bedtools=2.29.2

  - samtools=1.10

  - picard=2.23.3

  - macs2=2.2.7.1

  - fastqc=0.11.9

  - preseq=2.0.3

  - multiqc=1.9

  - ucsc-bedclip=377

  - ucsc-bedgraphtobigwig=377

  - subread=2.0.1
 
 No newline at end of file

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