Hello everyone.
I have started the "meat" of my data analysis and I'm already running into some problems.
I have Solexa (fq) data and I have attempted to align using Bowtie against the reference genome, only ~1% of the 5.8 million reads mapped to the genome. With this results I consulted the individual who sequenced our data to discover adapters were still attached. I used the fastx_clipper from the FastX Toolkit to remove the adapters and realign the data. The alignment processed for 9hrs, and did produce output, but the "-t" function did not list the % mapped and the % not mapped and the end of the run said "Segmentation Error".
brandon@brandon-desktop:~/bowtie$ bowtie -p 4 -t -a indexes/tair8 ~/Desktop/s_1_old.fq ~/Desktop/s_1_old.map
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
Seeded quality full-index search: 09:17:53
Time searching: 09:17:54
Segmentation Error
Does anyone know what that means? I've tried looking it up, but can't seem to find a reference to it anywhere.
Thanks,
Brandon
I have started the "meat" of my data analysis and I'm already running into some problems.
I have Solexa (fq) data and I have attempted to align using Bowtie against the reference genome, only ~1% of the 5.8 million reads mapped to the genome. With this results I consulted the individual who sequenced our data to discover adapters were still attached. I used the fastx_clipper from the FastX Toolkit to remove the adapters and realign the data. The alignment processed for 9hrs, and did produce output, but the "-t" function did not list the % mapped and the % not mapped and the end of the run said "Segmentation Error".
brandon@brandon-desktop:~/bowtie$ bowtie -p 4 -t -a indexes/tair8 ~/Desktop/s_1_old.fq ~/Desktop/s_1_old.map
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
Seeded quality full-index search: 09:17:53
Time searching: 09:17:54
Segmentation Error
Does anyone know what that means? I've tried looking it up, but can't seem to find a reference to it anywhere.
Thanks,
Brandon
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