Question: Please tell me what's wrong with my tophat script?
0
gravatar for abdul.suboor123
13 months ago by
Huazhong Agricultural University, China
abdul.suboor1230 wrote:

I am trying to find the unmapped reads by fusion-search in tophat, but When submit the command it shows some sort of warning, code is given below.

[skabdul@node102 Mo17]$ sh tophat.sh

[2018-11-06 20:00:15] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-11-06 20:00:15] Checking for Bowtie
          Bowtie version:    1.1.2.0
[2018-11-06 20:00:16] Checking for Bowtie index files (genome)..
[2018-11-06 20:00:16] Checking for reference FASTA file
    Warning: Could not find FASTA file ../Mo17/Ref-index.fa
[2018-11-06 20:00:16] Reconstituting reference FASTA file from Bowtie index
  Executing: /public/home/software/opt/bio/software/Bowtie/1.1.2-foss-2016b/bin/bowtie-inspect ../Mo17/Ref-index > M1_tophat_fusion/tmp/Ref-index.fa

Also check the command if there is something wrong in it or not?

/tophat-2.1.1.Linux_x86_64/tophat -o M1_tophat_fusion -p 12 --fusion-search --bowtie1 --keep-fasta-order --no-coverage-search ../Mo17/Ref-index M1_PE400_R1.fq M1_PE400_R2.fq
bowtie1 tophat bowtie2 • 473 views
ADD COMMENTlink modified 13 months ago by WouterDeCoster42k • written 13 months ago by abdul.suboor1230
1

I just drop this post from the senior developer here, so you may consider to change to a more recent tool like STAR or HISAT2.

enter image description here

ADD REPLYlink written 13 months ago by ATpoint26k

I think op is looking for fusion transcripts, which hisat lacks as of now. May be that user can use star fusion

ADD REPLYlink written 13 months ago by cpad011212k

I think there is no star-fusion , I am using tophat for circexplorer2 software, I search that websiter, the pipeline has not star-fusion.

ADD REPLYlink written 13 months ago by abdul.suboor1230

https://github.com/STAR-Fusion/STAR-Fusion/wiki

ADD REPLYlink written 13 months ago by cpad011212k

I am looking for fusion search to collect the unmapped reads. Its very slow I dont know whats the problem.

ADD REPLYlink written 13 months ago by abdul.suboor1230

are these solid reads? If not, let tophat use bowtie 2 instead of bowtie 1.

ADD REPLYlink written 13 months ago by cpad011212k
1
gravatar for WouterDeCoster
13 months ago by
Belgium
WouterDeCoster42k wrote:

The warning message is really clear:

Tophat expects to find ../Mo17/Ref-index.fa, but the fasta file is not there. Therefore it recreates the fasta file based on the Bowtie index. Everything runs normally.

ADD COMMENTlink written 13 months ago by WouterDeCoster42k

Thanks, but i have reference in fasta format. Then why it shows this warning? and tell me please it will create any problem? because even it shows warning but the program i running normally.

ADD REPLYlink modified 13 months ago • written 13 months ago by abdul.suboor1230
2

So you mean that ../Mo17/Ref-index.fa does exist? But no, this warning causes no problem. It just will run a bit slower because the fasta file has to be recreated from the indices.

For the record, I don't consider myself a "bro", but if that's how you want to address people online then go ahead.

ADD REPLYlink written 13 months ago by WouterDeCoster42k

Sorry for saying bro, It runs very slower, I have start running this job almost 12 hours ago, but till now it is running , I added -p 12 but with 12 cpu it is still very slow. Can you please mention how much time it takes normally?

ADD REPLYlink written 13 months ago by abdul.suboor1230
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