Question: Error: Could not find Bowtie 2 index files (p.*.bt2)
0
gravatar for sangita_b
3.3 years ago by
sangita_b70
United Kingdom
sangita_b70 wrote:

Hi,

I am repeating alignments using TopHat, I am using the same Bowtie index as I used previously (i.e I have successfully aligned reads using this index)

My command line is below:

tophat p 5 -G /home/msxakk/Desktop/NOT-BACKED-UP/iGenomes/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf -o 3a_q20 /home/msxakk/Desktop/NOT-BACKED-UP/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome 3aqtrimR1.fastq 3aqtrimR2.fastq

However the following error appears:

[2016-01-04 11:24:00] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2016-01-04 11:24:00] Checking for Bowtie
          Bowtie version:     2.2.3.0
[2016-01-04 11:24:00] Checking for Samtools
        Samtools version:     0.1.18.0
[2016-01-04 11:24:00] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (p.*.bt2)

 

Can anyone shed light on why Bowtie cannot locate/ use the index files?

 

Thanks Sangita

rna-seq • 3.5k views
ADD COMMENTlink modified 3.3 years ago by Devon Ryan89k • written 3.3 years ago by sangita_b70

Any particular reason you're using a version of TopHat2 that's a year and a half old?

ADD REPLYlink written 3.3 years ago by Daniel Swan13k
1

I trimmed my fastq files and noticed that when aligning these files the concordant alignment rate was 0.4% (for my other samples the alignment rate was 90-92%).

Long story short I am repeating the alignments and want to use the same version of TopHat that I used originally (I am worried that the trimming has affected the alignment).

Thanks

ADD REPLYlink written 3.3 years ago by sangita_b70
2
gravatar for Devon Ryan
3.3 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

You forgot the "-" in "-p 5".

ADD COMMENTlink written 3.3 years ago by Devon Ryan89k

Thanks Devon. I have added the  "-" in "-p 5" and now it works. it's always something small!

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by sangita_b70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1355 users visited in the last hour