Removing reads from data using Blast
1 answer
If you have fastq data then the best way to do this is use bbsplit.sh from BBMap suite to bin your reads. Read more about it here.
Log in to answer this question.
More posts like this
-
how can i determine the couverture (coverage ) of my reads on the whole genome using mapping (bowti…
written by Bioinfo •
-
How to build library in SSPACE
written by Bioinfo •
-
(Scaffolding ) Gap Closer - Gap Filler , SSPACE
written by Bioinfo •
-
The best k mer to use for illumina data
written by Bioinfo •
-
How to split fastq file containing Forward and Reverse reads to two files Forward and Reverse
written by Bioinfo •
-
Align reads files with diffrent number of reads using bowtie2
written by Bioinfo •
-
How can i extract unmapped reads using blast
written by Bioinfo •
-
Remove contigs that are lower than 200
written by Bioinfo •
-
MUMmer . Global alignment
written by Bioinfo •
-
How To Remove Contaminated Scaffold From Genome
written by raj.gzra •
You mean like in a xenograft, where host and graft cells get mixed up before sequencing? If not, how did the contamination happen?
I think you should be able to use BBSplit to separate reads from multiple organisms if you have the reference genome for each organism involved.
because i want to do assembly of endosymbiotic bacteria and it's probably contaminated by host mitochondrial dna