Commit dc28adce authored by TomKellyGenetics's avatar TomKellyGenetics
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update documentation for linkers

parent 07c2dda5

README.html

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<section class="page-header">

<h1 class="title toc-ignore project-name">UniverSC: Single-cell processing across technologies</h1>

<h4 class="author project-author">S. Thomas Kelly<sup>1†</sup>, Kai Battenberg<sup>1,2†</sup>, Makoto Hayashi<sup>2</sup>, Aki Minoda<sup>1</sup> <br> <sup>1</sup> RIKEN Center for Integrative Medical Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama <br> <sup>2</sup> RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama <br> † These authors contributed equally to this work</h4>

<h4 class="date project-date">Wednesday 08 July 2020</h4>

<h4 class="date project-date">Thursday 09 July 2020</h4>

</section>
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</div>



<section class="main-content">

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<p><img src="data:image/svg+xml;charset=utf-8;base64,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" alt="Docker Stars" /> <img src="data:image/svg+xml;charset=utf-8;base64,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" alt="Docker Pulls" /> <img src="data:image/svg+xml;charset=utf-8;base64,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" alt="Docker Image Version (latest by date)" /></p>

<div id="universc" class="section level1">

<h1><span class="header-section-number">1</span> UniverSC</h1>

README.md

+1 −1
Original line number Diff line number Diff line
@@ -6,7 +6,7 @@ affiliations: 
   index: 1

 - name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan"

   index: 2

date: "Wednesday 08 July 2020"

date: "Thursday 09 July 2020"

output:

  prettydoc::html_pretty:

       theme: cayman

launch_universc.sh

+7 −3
Original line number Diff line number Diff line
@@ -1663,6 +1663,7 @@ else 
    echo "  UMIs: ${umiadjust}bps at its tail" 

    

    #for CEL-Seq2 swap barcode and UMI

    ## https://github.com/BUStools/bustools/issues/4

    if [[ "$technology" == "sciseq" ]]; then

        for convFile in "${convFiles[@]}"; do

            #swap UMI and barcode
@@ -1738,6 +1739,7 @@ else 
    fi



    #remove adapter from SureCell (and correct phase blocks)

    ## https://github.com/Hoohm/dropSeqPipe/issues/42

    if [[ "$technology" == "surecell" ]]; then

        for convFile in "${convFiles[@]}"; do

            #remove phase blocks and linkers
@@ -1754,7 +1756,8 @@ else 


    # SPLiT-Seq can be set up similarly if a whitelist and 18bp barcode can be supported

    ## https://github.com/hms-dbmi/dropEst/issues/80

    if [[ "$technology" == "surecell" ]]; then

    ## https://github.com/sdparekh/zUMIs/wiki/Protocol-specific-setup

    if [[ "$technology" == "splitseq" ]]; then

        for convFile in "${convFiles[@]}"; do

            #remove phase blocks and linkers (swap UMI and barcode)

            sed -E '
@@ -1769,6 +1772,7 @@ else 
    fi



    #remove adapter from SCRB-Seq

    ## https://teichlab.github.io/scg_lib_structs/methods_html/SCRB-seq.html

    if [[ "$technology" == "scrbseq" ]]; then

        for convFile in "${convFiles[@]}"; do

            #remove adapters

man/convert.sh

+1 −1
Original line number Diff line number Diff line
@@ -137,7 +137,7 @@ Provides a conversion script to run multiple technologies and custom libraries w 


                /usr/local/bin/bcl2fastq  -v --runfolder-dir "/path/to/illumina/bcls"  --output-dir "./Data/Intensities/BaseCalls"\

                                             --sample-sheet "/path/to/SampleSheet.csv" --create-fastq-for-index-reads\

                                             --use-bases-mask y26n,I8n,I8n,Y50n  --mask-short-adapter-reads 0\

                                             --use-bases-mask Y26n,I8n,I8n,Y50n  --mask-short-adapter-reads 0\

                                             --minimum-trimmed-read-length 0



            Note that dual indexes are not supported by cellranger. Manually demultiplexing as above into separate

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