Overwrite Read sequences in bam with reads from Fastq
I had to modify my original reads (masking few nucleotides), now my alignment went well (i use bowtie2) but I need my original reads in my sam. So I need to catch the original read from my fastq to reinject it into my bam (I know the cigar would be compromised but I don't care).
What would be the most efficient?
My idea would be to use python to parse the fastq and the bam with Python (using pyfastx and pysam), but I'm wondering if something more efficient already exist.
• 1,026 views
•
link
updated
by
Istvan Albert
•
written
by
Juke34
•
written
by
Juke34
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How To Get Millions of Sequences from Genomic Regions Efficiently
written by Yacob •
-
Add Cigar string and Template Length to Read Name
written by Leendert •
-
Extracting CIGAR string from a specific region of a read in a bam file using pysam?
written by kiki4133 •
-
calculate fragments depth with pysam
written by electronsource75 •
-
Extracting descriptive metrics from variant reads in BAM
written by ognjen011
-
Random extraction of restriction enzyme target sites from whole genome
written by cfarmeri
-
pysam: filtering reads based on flag
written by QVINTVS_FABIVS_MAXIMVS
-
Extract specific reads from FASTQ files based on subsequence
written by Paul
-
Getting number of mismatches from bam record
written by noah •
-
Library To Parse Absolute Reference Positions Of Indels From A Bam Cigar String
written by William
this is a pretty esoteric need that also makes the BAM file invalid ... it is unlikely that any such tool would exist.
I am mainly chiming in to suggest another Python package that you could do it with - SimpleSam, it is pure python but needs samtools if operating on BAM file
https://simplesam.readthedocs.io/en/latest/