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. :)
1 answer
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.
Log in to answer this question.
-
RNA-Seq
written by prs •
-
RPKM normalization
written by prs •
-
How to remove introns in a specific nucleotide sequence
written by LeeLee •
-
Strandedness of RNAseq data from SAM alignment flag
written by rs.yousaf •
-
Write free text comment with @CO in BAM file
written by mhasa006
-
Extracting nucleotide immediately prior to mapped read
written by graeme.thorn
-
Gene specific region visualization in Alignment (.bam) or Variant calling file (.vcf) in IGV
written by ravi.uhdnis
-
How to get Allele Coverage from bam file or vcf file?
written by murali
-
How to over come "TypeError: argument of type 'int' is not iterable" in python?
written by murali
-
Bowtie Fp And Fn - How To Find ?
written by Arpssss •
