Question: How To Interpret Crossbow Data
0
gravatar for bashwin.u
6.1 years ago by
bashwin.u40
bashwin.u40 wrote:

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

genome paired-end mapping • 1.6k views
ADD COMMENTlink modified 4.8 years ago by shalini.ravishankar0 • written 6.1 years ago by bashwin.u40
0
gravatar for Devon Ryan
6.1 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

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).

ADD COMMENTlink written 6.1 years ago by Devon Ryan92k

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?

ADD REPLYlink written 6.1 years ago by bashwin.u40

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.

ADD REPLYlink written 6.1 years ago by Devon Ryan92k

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.

ADD REPLYlink written 6.1 years ago by bashwin.u40
0
gravatar for shalini.ravishankar
4.8 years ago by
shalini.ravishankar0 wrote:
@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
ADD COMMENTlink written 4.8 years ago by shalini.ravishankar0
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