Thank you will look into this.
• 0 views
•
link
written
by
blake.mcmurray •
Attaining subset of reads from fastq file that are mapped in alignment
Hello,
I am interested in pulling a subset of reads from a large fastq file that are mapped during an alignment I run. For example, I wish to run an alignment on the large fastq file and make a new smaller fastq file that contains all the reads that mapped in the alignment. I would greatly appreciate any assistance you may offer.
Kind regards,
Blake
• 1,268 views
•
link
updated
by
Ram
•
written
by
blake.mcmurray •
•
written
by
blake.mcmurray •
1 answer
Check samtools fastq and its option to only include certain reads using flags. Flags are explained here. https://broadinstitute.github.io/picard/explain-flags.html
Log in to answer this question.
More posts like this
-
Large FASTQ file processing failure: MetaPhlAn 3.0.7 + HUMAnN on 16-core 64GB system
written by chatterjeejayeeta100 •
-
Filtering reads from aligned scRNA reads BAM file by filtered cells barcodes (CB)
written by MYousry •
-
Removing a subset of fasta reads from a huge fastq file
written by resug •
-
Tracking Down Reference Database For Alignment
written by blake.mcmurray •
-
General Tips On Using Optimal Alignment Flags For Specific Data
written by blake.mcmurray •
-
How to use mafft to do large scale sequence alignment?
written by sunyeping •
-
how to take the subset of fastq reads in one specific chromosome
written by jolin0701-dy
-
BWA alignment issue in iPlant
written by aj123
-
sra toolkit program fastq-dump question.
written by jinhwa1112 •
-
Do Aligners Tend To Scale With Number Of Bases Or With Number Of Reads?
written by Ian •
Have you looked at samtools?