fastx barcode splitter failed to create output file

Question

[xiao.liu]

Hi all, I was trying to use the fastx barcode splitter to demultiplex my RNA-seq results, but when I tried to run the command below:

$ cat lane1_Undetermined_L001_R1_033_trimmed.fq | fastx_barcode_splitter.pl --bcfile barcode_list.txt --bol --prefix /demultiplexed/33_

the terminal responds:

Error: failed to create output file (/demultiplexed/33_unmatched)

cat: write error: Broken pipe

I'm very new to this and couldn't figure out why. Could someone kindly provide some suggestion? Thank you very much in advance!

Answer 1

[GenoMax]

You may want to try BBMap for this. Based on the name of your file I assume this is standard Illumina data. You would use demuxbyname.sh program.

demuxbyname.sh in=r#.fq out=out_%_#.fq prefixmode=f names=GGACTCCT+GCGATCTA,TAAGGCGA+TCTACTCT,... outu=filename

names= can also be a text file with one barcode per line (in exactly the format found in the read header). You do have to include all of the expected barcodes.

In the output filename, the "%" symbol gets replaced by the barcode; in both the input and output names, the "#" symbol gets replaced by 1 or 2 for read 1 or read 2. Specify in1= in2= out1= out2= if you want custom naming.