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Illumina / isaac2

Aligner for sequencing data
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Aligned reads only have 25 bases. #7

Closed zeus19900814 closed 9 years ago

zeus19900814 commented 9 years ago

Hi Come,

Sorry to bother you so often. Without changing any default parameter values, aligned reads in output bam always only have 25 bases. Is it because the parameter --base-quality-cutoff? I changed it to different value but the number of bases in aligned reads still didn't change.

Please advise how I can keep the original read bases without trimming them in bam file.

Thank you so much! Ivan

rpetrovski commented 9 years ago

if you are aligning from fastq, iSAAC automatically picks the read length from the first pair of reads it sees. if you want a different one, you need to use --use-bases-mask yA,yB for paired data or --use-bases-mask yA for single-ended.

Where A and B are correspondingly read lengths for read one and two.

Roman.

On Thu, Aug 27, 2015 at 8:42 PM, zeus19900814 notifications@github.com wrote:

Hi Come,

Sorry to bother you so often. Without changing any default parameter values, aligned reads in output bam always only have 25 bases. Is it because the parameter --base-quality-cutoff? I changed it to different value but the number of bases in aligned reads still didn't change.

Please advise how I can keep the original read bases without trimming them in bam file.

Thank you so much! Ivan

— Reply to this email directly or view it on GitHub https://github.com/Illumina/isaac2/issues/7.

zeus19900814 commented 9 years ago

Thanks, Roman!

What if I don't have a preference on read lengths? I just want to keep all the original bases?

rpetrovski commented 9 years ago

Then you probably should find the longest read in your fastq and use it with --use-bases-mask. iSAAC was designed to primarily process bcl and with bcl the read length is pretty straightforward.

On Thu, Aug 27, 2015 at 9:04 PM, zeus19900814 notifications@github.com wrote:

Thanks, Roman!

What if I don't have a preference on read lengths? I just want to keep all the original bases?

— Reply to this email directly or view it on GitHub https://github.com/Illumina/isaac2/issues/7#issuecomment-135537658.

zeus19900814 commented 9 years ago

I see!

Really appreciate your help!