Thanks for your efforts ! Luckily, I have just solved this problem by changing
the source code "maxcnt = 8000" to "maxcnt = 80000" in
"samtools-1.3.1/htslib-1.3.1/sam.c.
Best,
Yudong
At 2017-03-05 00:00:05, "Dario Beraldi" <dario.bera...@gmail.com> wrote:
Hi Yudong,
I can't answer your question and apologies to the list for hijacking this
thread. Depending on your needs, you may find useful ASCIIGenome
(http://asciigenome.readthedocs.io/en/latest/ - full disclosure: I'm the
author).
To save the aligned reads in a region to a text file you can do:
ASCIIGenome -ni -r chr7:5566726 -fa genome.fa -x 'trackHeight 100000 bam@ &&
save output.txt' aln.bam > /dev/null
Explained: read file aln.bam and use genome.fa as reference. Go to position
chr7:5566726. Then execute the commands inside the -x '...' string: Set track
height to 100000 lines of text (i.e. a number large enough to include all the
reads) for the track name containing 'bam@' (i.e. the track of aligned reads).
Then save the view to file output.txt.
Note that at the moment ASCIIGenome is quite a bit slower then samtools tview
and insertions to the reference are not shown (among genome viewers I think
tview is the only one able to do that). However, ASCIIGenome is more flexible
than tview.
Hope this helps
Dario
On 2 March 2017 at 12:31, huyudong <huyudon...@126.com> wrote:
Hi,
Recently, I have used samtools tview -d T -p position data.sort.bam
--reference genome.fasta to get all the reads alignment text file. But it
seems that the maximum read alignment number in tview is about 8000+, and my
remaining aligned reads are not shown. I wonder if the samtools tview has the
maximum read alignment number limitation and how to expand the tview to show
as many alignment reads as possible. Looking forward to your reply, thank you
very much !
Best,
Yudong
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