How To Interpret Crossbow Data

Question

[bashwin.u]

Hello,

May I know how to interpret Crossbow output. Is there any chance of building a SAM or BAM file from Crossbow output. I am looking into genome mapping. I know there are many tools available for genome mapping on hadoop cluster. But I like the Crossbow interface, very easy to use.

PS: I dont have a background in Bioinformatics. I am an IT student working on Hadoop infrastructure to assess its performance for an organization.

Thanks

Answer 1

[Devon Ryan]

The primary output of crossbow is a file giving evidence for SNPs (the format is described in the Crossbow manual, which is simply that of SOAPsnp). I believe that the alignment files are deleted by default, but you should be able to have them kept with either the --keep-intermediates or --keep-all flags (make sure to specify an appropriate output path).

[bashwin.u]

Have you used crossbow before? May I know what are the intermediate files generated while running crossbow? Just read from Crossbow FAQ that SAM/BAM files are not generated as intermediate files. Do you know if there is any chance of building SAM/BAM files from Crossbow output or intermediate files?

[Devon Ryan]

No, but my understanding from elsewhere is that while the alignments aren't saved normally, they're intermediate files that can still be saved with --keep-all. That makes sense given that SOAPsnp needs something as input.

[bashwin.u]

yea definitely the intermediate files can be saved using those flags. But according to Crossbow manual those intermediate files are not in SAM or BAM format. And i tried looking for the intermediate files on the internet, I cant get hold of any info about it.

Answer 2

[shalini.ravishankar]

@bashwin.u hi ashwim, im in a similar situation. Can u please tell me how did u store the bam files on hadoop cluster so that the data will be processed by chromosome level