Error: Could not find Bowtie 2 index files (p.*.bt2)

Question

[sangita_b]

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

[User 59]

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

[sangita_b]

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

Answer 1

[Devon Ryan]

You forgot the - in -p 5.

[sangita_b]

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