How To Specify The Target Database For The Trinity_Alignreads.Pl Script

Question

[nbvasani]

Hello Fellows,

I trying to run read alignment using trinity script that is alignreads.pl. I used the command below:

/bin/util/alignReads.pl \
  -seqType fq \
  -single inputfile_name \
  -target Trinity.fasta \
  -aligner bowtie2 \
  -p 4 \
  -retain_intermediate_files \
  -num_top_hits 20 \
  -output align_bowtie_output
`

but I am getting below error:

Must specify target_db and it must exist at that location at /bin/util/alignReads.pl line 180

I don't know what does that mean, as I am not good with reading script.

Hope you guys can help me out.

Thanks,
Naresh

Answer 1

[Dan D]

It looks like you may need to specify the full path to your FASTA file instead of just the name. I also recommend putting two dashes in front of your seqType, single, target, aligner, retain_intermediate_files, num_top_hits and output parameters as well.

[nbvasani]

Hi Deedee, After placing two dashes and specifying full path. It work fine with one error about aligner. So i guess problem was with aligner bowtie2. It actually has only bowtie aligner and not bowtie2.

Thanks, Naresh

[Dan D]

Cool, glad to hear it! Don't forget to accept the answer if it indeed resolved your question.