If you want to get rid of the pair used bedtools pairtobed -a bam -b rRNA.bed
-type either
There are other options in pairtobed you can use and the bam automatically get
changed into bedpe format where you can then filter on mq.
On Sep 30, 2014, at 9:18 PM, Nils Homer wrote:
> Hey Bow,
>
> u
bedtools intersect -abam (bam) -b rRNA.bed -v should be able to handle this.
On Sep 30, 2014, at 9:18 PM, Nils Homer wrote:
> Hey Bow,
>
> unfortunately there is no single tool that would perform your task. While
> you could try to chain various tools together, the difficulty in this process
Hey Bow,
unfortunately there is no single tool that would perform your task. While
you could try to chain various tools together, the difficulty in this
process is to make sure that the mate information for paired reads is
updated correctly. If you want some tips on developing such a tool for
yo
Hi,
I am using bwa mem align 454 fasta file to a reference genome and
"samtools mpileup -ugf ref.fa 454.bam" to generate the BCF format.
However, it throws a core dump error.
Does the samtools mpileup (v1.1) required quality information in the
bam/sam file? In other words, the alignment step shoul
On Sep 29, 2014, at 22:13 , Mengmeng Lu wrote:
> Exception in thread "main" htsjdk.samtools.SAMException: Exception closing
> FileOutputStream for
> /data/mira0501/agilentfastq/nonmulti/mira0501/CSPI.5751822609546779855.t
> mp/27421.tmp
I bet you're running out of disk space for the temporary f
Hi Kevin - what is the command you are running?
Thomas
On 9/29/14, 7:34 PM, Koh, Chushin wrote:
> Hi all,
>
> I have a very fragmented reference genome (>million scaffolds) that I was
> able to call variants using Samtools-mpileup V0.19. However, V1.1 hanged on
> the same data set with no error
Hi all,
I have a very fragmented reference genome (>million scaffolds) that I was able
to call variants using Samtools-mpileup V0.19. However, V1.1 hanged on the same
data set with no error produced, just never run to completion. The V1.1 still
does not work if I extract alignments on a small s
