How to align mouse transcriptome data using bowtie2?

Question

[John]

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

[Tom_L]

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/

[John]

Thanks a lot! I found them!

[Buffo]

cat *.fasta > single_file.fa

[John]

I dont understand, Is this command for combining all fasta files after downloading for each chromosome?

is this a only procedure?

[Buffo]

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.

[WouterDeCoster]

bowtie2 is not an appropriate aligner for an eukaryotic transcriptome experiment

[John]

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

Answer 1

[John]

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!