How to extract and cut sequence from a given region from a BAM file
Hi,
I have an aligned BAM file and I want to extract sequence from a given region and just that, not what's come after or before the specific region.
I try samtools with:
samtools view -b alignment_sort_JX888104.bam "JX888104.1:569-895" > filt_aln_grp1_JX888104.bam
but it give me all the read that comes in this interval even if it's one base.
After that I try bedtools:
bedtools intersect -wa -a alignment_sort_JX888104.bam -b grp1.bed > test_intersect_grp1.bam
with
grp1.bed -> JX888104.1 569 895
but it give me an error that my bed is not recognize.
Do you have another idea?
Thanks in advance
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ATpoint
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nbargues •
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see Limiting variant calls to amplicon target regions? ; tool for bam soft clipping reads within bed file regions
what is the output of
?
ASCII text
JX888140.1 569 895
you're not using a tab as the column separator but spaces.
Output should have been
furthermore, if your bam interval was "JX888104.1:569-895" , then your bed should have been
see What Are The Advantages/Disadvantages Of One-Based Vs. Zero-Based Genome Coordinate Systems
you're right, I thought that with atom tab was imply but apparently not, thanks. I fix that and I don't have the bedtools error anymore but when I look the data on IGV, I still have all my reads.
am I doing something wrong with my bedtools command ?
Cheers