Fastx-barcode_splitter.pl

[shis]

Hello,

I would like to use fastx_barcode_splitter.pl to creat individual read files for each samples, and have typed the following command in terminal. It has been separated each samples but also showed error. I also got one file that is containing unmatched.fq file which is 10.9 MB of the input file 19.6 MB.

$ cat par.r1r2.fq | fastx_barcode_splitter.pl --bcfile barcodes.txt --bol --prefix "par." --suffix ".fq"
Error: bad input file, expecting line with sequence name2



Can anyone advice me how can I get rid of this error? Thank you.

[GenoMax]

Is the error indicating a specific line in your sequence file? Perhaps you have a malformed sequence ID line.

[shis]

Hi GenoMax,

Thanks for your reply. I have just decompresses *.gz back to *.fq file. I had three files namely, parent, progeny and strip. Progeny and strip worked perfectly fine, but error shows only in case of parent although I did same for all three files.

[GenoMax]

Can you try to validate the fastq file (http://genome.sph.umich.edu/wiki/FastQValidator) to see if it spots the problem header line?