@@ -61,6 +61,11 @@ But note that the the processing of SAM files is not fully optimized and can be
```sh
chromap -x index -r ref.fa -1 query1.fq,query2.fq,query3.fq --SAM-o alignment.sam
```
Chromap also supports wildcards in the read file names and will find all matched read files. To use this function, the read file names ***must*** be put in quotation marks:
```sh
chromap -x index -r ref.fa -1"query*.fq"--SAM-o alignment.sam
```
Chromap works with gzip'd FASTA and FASTQ formats as input. You don't need to convert between FASTA and FASTQ or decompress gzip'd files first.
***Importantly***, it should be noted that once you build the index, indexing parameters such as **-k**, **-w** and **--min-frag-length** can't be changed during mapping. If you are running Chromap for different data types, you will probably need to keep multiple indexes generated with different parameters.
