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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