Reference genome for BOWTIE2
I was working on EBI: Next Generation Sequencing Practical Course. Here in the first step to align the RNA-Seq data to the genome using BOWTIE2 we need a reference genome. The reference genome as I found comes as fragmented fasta file for each chromosome. I guess we need a combined file; where do I get it? Or is there a method to concatenate each file?
• 3,272 views
•
link
updated
by
Sej Modha
•
written
by
Arindam Ghosh
•
written
by
Arindam Ghosh
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
News: Spring School in Bioinformatics – Online Course, 8–12 June
written by Physalia-courses
-
Combining and Forward and Reverse Reads
written by SineWave •
-
Bowtie2 or Bowtie
written by priscilladraj •
-
Snpcalling with replicates
written by eyonesi •
-
Best way to assemble a genome with a reference
written by genseq •
-
HiSat2 vs BowTie2 for mapping miRNA-seq reads
written by Arindam Ghosh
-
Threshold in WGCNA
written by Arindam Ghosh
-
Mapping /aligning reads to a custom genome
written by Adeler001 •
-
How to not penalize a specific mismatch when aligning?
written by ervaulsy •
-
How To Get Snps Matrix For Population Genetic Ananlysis From Snps Variant Files
written by Jianfengmao •
Bowtie2 is compatible with multiple reference fasta file. It should work just fine with the reference file you have downloaded.
Multiple reference fasta file? So do I need to list the names of all the files containing each individual chromosome.
is same as multiple sequences in a fasta file. Apologies for poor choice of terminology.
You can concatenate the files together with a simple
cat *.fa > /path_to/new.facommand (putting the combined file someplace else so the command would not try to include it in the originalcat).Well I guess I found a way out. The database also contains something called Top-level sequence and Primary Assembly that is actually supposed to be used.