Calculating fragment start and end in python
I'm trying to calculate the fragment information for Illumina pair-end sequences. For that, I need to calculate the fragment start and fragment end. There are two ways I'm calculating the fragment start/end
fragmentStart = min(read.pos, read.pnext) + 1
fragmentEnd = fragmentStart + abs(read.isize)
and the second
fragmentStart = read.reference_start
fragmentEnd = fragmentStart + abs(read.isize)
Can anybody tell me which one is the correct way? Also, how can I verify the numbers I'm getting? Currently, I'm trying to manually check the BAM files to find the positions.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
RNA-seq: identifying pericentromeric region
written by Polly •
-
Trying to work with the NCBI's Entrez api using python.
written by gdizzle12 •
-
Issue softclipping reads when they belong and don't belong to a common amplicon
written by ManuelDB
-
Esearch, Epost, and Efetch for Large Datasets in Biopython
written by Salem •
-
insert size in bam file do not make sense
written by ccagg
-
Counting single-cell ATAC fragments at peaks on BED file
written by Nico •
-
How to efficiently get reference bases (hg19) for a list of SNV loci (e.g., from a MAF file)?
written by mrz132435 •
-
calculate fragments depth with pysam
written by electronsource75 •
-
MACS2 Nomodel doesnt take the fragment size
written by GK1610
-
Extracting exons from CDS CompoundLocations of a genbank file
written by lhirsch •
would
bedtools bamtobedget you what you want? https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.htmlActually, I'm fetching reads form a BAM file that is within a bed region. Then I'm trying to calculate the fragment start/end of the fetched reads
how about filtering the BAM file for the region on interest and then converting the output to a BED file which will contain the read start and stop coordinates?
Thanks for the reply, will try that.
Do you need to to this in python? There are tools already out there performing these kind of tasks, such as CollectInsertSizeMetrics (picard)
Well, that is true, but it is part of a bigger project. And calling third-party tools can be problematic. Either way, thanks for the reply.