Question: Get the positive and negative strands of reads in bam file for particular nucleotide position?
0
gravatar for murali
4.1 years ago by
murali90
Germany
murali90 wrote:

Get the positive and negative strands of reads in bam file for particular nucleotide position?

For example, If I have the bam file contains Chromosome:3  nucleotide_position:13226978, I want to find the no of reads mapped to particular nucleotide_position. It can be done by the pysamstats package using reads_all function.

Now, I want to find out positive and negative strands or reads to that particular nucleotide_position as well as gene-symbol associated with it?

How can I do this and can able extract relevant information?

I want to do it for list of bam files, so I am writing python script.

Any suggestions  related to  extracting strands as well as gene-symbol are really helpful to me. :)

 

sequencing pysamstats strands • 1.8k views
ADD COMMENTlink modified 4.1 years ago by Devon Ryan89k • written 4.1 years ago by murali90
1
gravatar for Devon Ryan
4.1 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

For getting a count of the orientation of alignments overlapping a position, you would use pysam with the pileup() function. You would then iterate over the PileupReads returned for a given position and increment a counter if an alignment is reverse complemented.

For the annotation aspect, pybedtools would be the logical choice if you're already writing stuff in python.

ADD COMMENTlink written 4.1 years ago by Devon Ryan89k
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