Question: Trouble With Kb1454Chr5.Bam, Bushman Chrm5, 454 Data Only
0
gravatar for Allan Lindh
5.4 years ago by
Allan Lindh10
Allan Lindh10 wrote:
Sorry to bother you with this, but I am trying to process the KB1 Bushman data, through a pipeline that starts with samtools mpileup -C50 -uf ~/Bushman/hg18/chromFa/chr1.fa ../KB1illumChr1.bam ../KB1454chr1.bam | bcftools view -c - Processing the data one cromosome at a time, aligning the data against hg18, using mpileup to combine the illumina and 454 data. All goes very well, everything looks good all the way through, results are stable, hi-quality, and conceivably even meaningful, except for KB1454chr5.bam, the 454 data for Chrm5 When combined with the illumina data for Chrm5 it results in garbage, even though if I run the illumina data alone, it looks like all the other Chromosomes. I confess that I am worse than a Newbie, I'm an old guy working on my own, so may in fact just be in way over my head. But if there is any chance you could take a look at KB1454chr5.bam to see if there were a lot of bad reads, or an error was made in processing, or anything else is wrong, I'd be most grateful.
mpileup samtools bam • 492 views
ADD COMMENTlink written 5.4 years ago by Allan Lindh10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 141 users visited in the last hour