On Thu, 28 Aug 2014 16:36:11 -0400
Nils Homer wrote:
> Could it be because we search for the associated sequence dictionary
> using the fasta file name, and the dictionary it finds for one is
> missing or mismatching? You could search for *.dict or *.fai files
> for each path.
Right again. It's
Hi Mark,
It would be helpful if you showed the exact command used and also how you
confirmed that an alignment was lost. Just this week I saw a post (elsewhere)
where someone was losing reads in converting from SAM->BAM only to find that it
was due to misusing an obscure (present but undocument
Hello,
We have been comparing whole genome sequence bam files and we have found
that samtools sort -n either removes or modifies the reads as it sorts. We
have tried it on both the older version and version 1.0 and have had the
same results. We found that several reads are in our original file,
Could it be because we search for the associated sequence dictionary using
the fasta file name, and the dictionary it finds for one is missing or
mismatching? You could search for *.dict or *.fai files for each path.
N
On Thu, Aug 28, 2014 at 3:50 PM, Jeremy Volkening
wrote:
> Well, that did
Well, that did the trick. I had given up on providing the reference
sequence because it always crashed picard with:
Exception in thread "main" java.lang.NullPointerException
at
htsjdk.samtools.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:87)
at
picar
Try giving it a reference sequence (R=...) to see if the alignment-based
metrics are output.
N
On Thu, Aug 28, 2014 at 2:35 PM, Jeremy Volkening
wrote:
> Hello,
>
> I have a set of ~ 1 billion gDNA paired reads mapped to a reference
> genome with BWA-MEM. I tried to use picard's
> CollectAlign
Hello,
I have a set of ~ 1 billion gDNA paired reads mapped to a reference
genome with BWA-MEM. I tried to use picard's
CollectAlignmentSummaryMetrics to generate a summary of the mapping,
but it reports zero aligned reads:
FIRST_OF_PAIR 549154663 549154663 1 0 0 0 0 0 0 0 0
Hi Radhouane,
You'll need to install the ncurses development library for your platform to
compile the tview command.
I believe you'll need ncurses-devel on Fedora/RHEL or libncurses5-dev on
ubuntu.
Sam
On Wed, Aug 27, 2014 at 6:20 PM, Radhouane Aniba wrote:
> Hello
>
> I wanted to try samtools
