Question: Questions about using Bowtie2
gravatar for fk566938
3.7 years ago by
United States
fk56693810 wrote:

Hello I am a Research Technician doing some bioinformatics which isn't something I've had prior experience in. I am using Bowtie 2 and I am aligning RNAseq files downloaded from the illumina bodymap website (16 tissues) to hg19 index files that were created in bowtie2. This is the message I get from the alignments:

-bash-4.1$ bowtie2 -p 22 -x software/bowtie2-2.2.6/scripts/hg19 -U ERR030858.fastq -S 030858.sam                             77229855 reads; of these:
  77229855 (100.00%) were unpaired; of these:
    29907119 (38.72%) aligned 0 times
    30792402 (39.87%) aligned exactly 1 time
    16530334 (21.40%) aligned >1 times
61.28% overall alignment rate

I am not sure if this is good or bad, if I'm getting the right thing or not. Is there any way of knowing?


linux rna-seq bowtie2 software • 1.1k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by fk56693810
gravatar for Antonio R. Franco
3.7 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.1k wrote:

Bowtie2 is not splicing aware. If you used the whole genome as reference, it contains introns, and all of the reads that are spliced, will be unmapped

Use a splice aware program such as TopHat, STAR, BBMap, Kallisto, etc to do the mapping

ADD COMMENTlink written 3.7 years ago by Antonio R. Franco4.1k

do you know what the command would be for tophat? I have it loaded, however I've never used linux before and so all of this has been quite a challenge for me.

ADD REPLYlink written 3.7 years ago by fk56693810

Tophat has many choices, but after installing the program you can run the following

tophat >& help.tophat

less help.tophat

And you will have the chance to read the instructions

ADD REPLYlink written 3.7 years ago by Antonio R. Franco4.1k
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