Dear Maraike. You may want to google bedtools coverage. This is a fantastic
toolbox which takes you bam too.SuccessStephane
Sent from my smartphone.
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samtools-help-requ...@lists.sourceforge.net Date: 6/24/17 14:04 (GMT+01:00)
To: samtools-help@lists.sourceforge.net Subject: Samtools-help Digest, Vol 101,
Issue 4
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Today's Topics:
1. Help with mpileup (Maraike Probst)
----------------------------------------------------------------------
Message: 1
Date: Fri, 23 Jun 2017 23:25:14 +0300
From: Maraike Probst <marai...@post.bgu.ac.il>
To: samtools <samtools-help@lists.sourceforge.net>
Subject: [Samtools-help] Help with mpileup
Message-ID: <92bec67d-a73c-a707-660b-58518c78f...@post.bgu.ac.il>
Content-Type: text/plain; charset=utf-8; format=flowed
Hello,
I am a newby, to this list and also to samtools. So, maybe I am missing
something very basic and I apologize in case this is trivial.
I created bam files aligning reads from several sequencing samples to a
set of queries (multifasta with a sequence length of around 5000 bp).
Which worked fine and the bam file did not cause any problems in
downstream analysis. Now I want to know the coverage of the reads on the
queries. So I sorted the bam file (using sort input.bam > sorted.bam, no
further settings) and created a mpileup file (using mpileup -s
sorted.bam > output.mpileup, I also tried -A parameter). Now I am having
the problem, that some of these mpileup files cannot be further
processed and to be honest, I have no idea why. From other analysis, I
know there are reads aligned, the files are fine, but the mpileup causes
problems. Viewing the mpileup file, just to try if it can be read,
resulted in the error
[E::sam_parse1] missing SAM header
[W::sam_read1] parse error at line 1
[main_samview] truncated file.
Any suggestions why? And how to solve this problem?
Probably, I need to provide more information, but I don't know which
information is required. Sorry for that. I am happy to give more infos
if specified.
Thanks a lot in advance. Feeling quite helpless here.
All the best,
Maraike
--
Maraike Probst, PhD
Mizrahi Lab
Department of Life Sciences
Faculty of Natural Sciences
Ben-Gurion University of the Negev
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