Extracting Reference Sequence from Bowtie Alignment
I am aligning a consensus sequence using bowtie2 and I would like to extract the sequence of the reference genome in the areas it aligns to. Is there an easy way to do this or include the reference sequence in the sam output of bowtie? Thanks!
• 103 views
•
link
written
by
eholleman •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Generate consensus from contig alignment to reference sequence
written by daewowo •
-
Bowtie2 adds insertions instead of allowing extention
written by chrisgr •
-
bash bowtie script output with prefix
written by Amaranta Remedios •
-
Reconstruct reference sequence from SAM file?
written by eholleman •
-
Help! Obtaining consensus sequence from Aligned BAM file
written by Peeham •
-
Piping bowtie2 output directly into BAM
written by hersh •
-
RNAseq consensus transcript sequence
written by Neuls •
-
Generate Consensus Sequence from Pairwise Alignment
written by kspata
-
Extracting the best reads that align multiple times
written by ioannis •
-
Querying hg19 reference genome
written by mdhale121 •
Hello eholleman!
Questions similar to yours can already be found at:
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!