I used trinity in iPlant to get a good assembly. However, I have since learned that I should use bowtie and RSEM for mapping and quantifying my transcripts. I successfully downloaded and ran "make" on the Trinity package from Sourceforge and uploaded my Trinity Fasta file and a couple of test fq files to work through the process. However, when I run the following command
horvathdp@128:/vol-8A5507EB/Trinity/trinityrnaseq_r20131110$ util/alignReads.pl --left 0Hr_1_R1.fq --right 0Hr_1_R2.fq --seqType fq --SS_lib_type RF \--target paradormancy_Trinity_contigs.fasta --aligner bowtie2 --retain_intermediate_files -- -p 8
I get this:
Error, path to required samtools cannot be found at util/alignReads.pl line 245.
horvathdp@128:/vol-8A5507EB/Trinity/trinityrnaseq_r20131110$
I ls'd the util file, and didn't see bowtie2. Is there some utility missing from the Trinity package that needs to be added separately,or some other functionality that I need to install? Any advice would be greatly appreciated.
Dave
horvathdp@128:/vol-8A5507EB/Trinity/trinityrnaseq_r20131110$ util/alignReads.pl --left 0Hr_1_R1.fq --right 0Hr_1_R2.fq --seqType fq --SS_lib_type RF \--target paradormancy_Trinity_contigs.fasta --aligner bowtie2 --retain_intermediate_files -- -p 8
I get this:
Error, path to required samtools cannot be found at util/alignReads.pl line 245.
horvathdp@128:/vol-8A5507EB/Trinity/trinityrnaseq_r20131110$
I ls'd the util file, and didn't see bowtie2. Is there some utility missing from the Trinity package that needs to be added separately,or some other functionality that I need to install? Any advice would be greatly appreciated.
Dave
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