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Old 12-30-2015, 10:39 AM   #2
Location: Santa Fe, NM

Join Date: Nov 2013
Posts: 20

Can anyone help me with this? Now I'm having the same result when I try to map single-fastq reads (multplexed-PE in this case) to the Maize AGPv3 genes. Run-of-the-mill application of TopHat2. Here's the command:

tophat --library-type=fr-unstranded --no-novel-juncs --transcriptome-only --transcriptome-index=tindex/AGPv3 -o SRR650377 /mnt/data/AGPv3/AGPv3 SRR650377.fastq.gz

I've already indexed the transcriptome, so I'm not using the -G option. (I was planning on running this against seven different samples.)

As before, this runs forever:

sam 23656 23652 0 Dec29 ? 00:00:00 perl /usr/local/bin/bowtie2 -x /mnt/data/AGPv3/AGPv3 /dev/null
sam 23658 23656 94 Dec29 ? 16:24:08 /usr/local/bin/../src/bowtie2/bowtie2-align-s --wrapper basic-0 -x /mnt/data/AGPv3/AGPv3 /dev/null
Sam Hokin
Computational Scientist, Carnegie and NCGR
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