"readFilesCommand" must be correctly set while running. From the STAR manual:
readFilesCommand:
string(s): command line to execute for each of the input file. This command should generate FASTA or FASTQ text and send it to stdout
For example: zcat - to uncompress .gz files, bzcat - to uncompress .bz2 files, etc.
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Hi Anthony,Santosh's suggestion is right to the point - if you add --readFilesCommand zcat to the STAR command line parameters, it will process the zipped FASTQ file.STAR does not support multi-line FASTQ files. There is a discussion going on whether FASTQ format allows for multi-line reads.On the other hand, STAR supports multi-line FASTA, so if you convert your multi-line FASTQ into FASTA, it should be OK.Cheers
Alex
On Tuesday, January 21, 2014 6:00:23 PM UTC-5, Anthony Colombo wrote:
> STAR does not support multi-line FASTQ files. There is a discussion going on whether FASTQ format allows for multi-line reads.
However, It is not difficult to convert them to "more standard" format using "seqtk"seqtk seq multi-line.fq > standard.fq
There are supposedly other tools which can do this conversion:(....In the list, seqtk, bioawk and seqret work with multi-line fastq; the rest don't...)
On Wednesday, January 22, 2014 9:34:34 PM UTC+1, Alexander Dobin wrote:
Hi Anthony,Santosh's suggestion is right to the point - if you add --readFilesCommand zcat to the STAR command line parameters, it will process the zipped FASTQ file.STAR does not support multi-line FASTQ files. There is a discussion going on whether FASTQ format allows for multi-line reads.On the other hand, STAR supports multi-line FASTA, so if you convert your multi-line FASTQ into FASTA, it should be OK.Cheers
Alex
On Tuesday, January 21, 2014 6:00:23 PM UTC-5, Anthony Colombo wrote: