How to align mouse transcriptome data using bowtie2?
Hi dear one,
I have previously aligned bacterial RNA-seq with its reference genome, it has only one chromosome! But for mouse I have found the reference genome (As well as transcriptome) for each chromosomes separately! I am now confused, Is it possible to get them in a single file, what is the usual procedure for aligning eukaryotic transcriptome!
Thanks in advance
1 answer
I found reference genome (mm9) at http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/ as mm10.2bit file and converted to fasta then! Thanks everyone!
I have a doubt that refMrna.fa.gz is the reference transcriptome file?
Please reply with whether both are right or wrong!
Thanks in advance!
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cat *.fasta > single_file.fa
I dont understand, Is this command for combining all fasta files after downloading for each chromosome?
is this a only procedure?
Absolutely It depends what are you looking for, but if you want to analyze the complete transcriptome, you have to concatenate all chromosomes in a single fasta file (cat *.fasta > single_file.fa) and then align the reads exactly in the same way as you have already done for one chromosome.
You can either concatenate all chromosomes into a single file or download a single file that directly contains all chromosomes. Usually, software work with a single file as it is simpler to handle. See here for mm10 genome version: http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/
In this link there are lots of file, but I don't understand which one is reference genome and which one is reference transcriptome! (I want both)
Can you please help me!
Thanks alot! I found them!
Thanks a lot! I found them!
bowtie2 is not an appropriate aligner for an eukaryotic transcriptome experiment
Yeah I checked that But I am planning to use RSEM which uses Bowtoe2 only right? thats why I mentioned as Bowtie2! Thanks for your response