bowtie2 and FLASh
I was wondering whether there is a proper way of using bowtie2 after going through my reads with FLASh (https://ccb.jhu.edu/software/FLASH/). Flash would produce 3 files:
- extended fragments
- non extended R1 fragments
- non extended R2 fragments
I could call bowtie2 twice (one for the extended fragments, one for the R1/R2 reads) and then merge the two sam (or bam) files, though I get the feeling the -U option in bowtie2 might allow me to do something smarter? am I missing something? being able to input all 3 files at once would be faster/simpler, and thus preferable if possible (I accept it might not).
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Treating forward and reverse reads independently in BWA
written by shpak.max •
-
kraken2 unclassified output does not work with paired reads?
written by DNAngel
-
bowtie2 --un vs --un-conc
written by blur
-
Bowtie: Mate files mapping error
written by priya.dalvi •
-
Should I merge the Paired-end RNA-seq reads for BLAT for intron identification
written by praasu •
-
bbmerge merged read smaller that original reads
written by snishtala03 •
-
RadSeq and short read
written by gbl1
-
From pooled fastq data to SNPs
written by Fedster •
-
Weird fragments when aligning PE reads to duplicated genes.
written by bsksln •
-
paired end illumina reads
written by midox
I would say: or you use only
extended fragmentsor you do not use FLASH.But besides this, maybe this helps Should I merge forward and reverse reads before mapping
I asked Julian Catchen (who wrote Stacks) and he recommends NOT using it.