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YeoLab / gscripts

General Use Scripts and Helper functions
MIT License
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Sailfish quant failing in pipeline #82

Open gpratt opened 8 years ago

gpratt commented 8 years ago 
sailfish_quant.py '-1' '/projects/ps-yeolab2/for_anthony/analysis/av_mouse_stress_v1/AV_stress_q331K_b_S18_L008_R1_001.polyATrim.adapterTrim.rep.bamUnmapped.out.mate1'  '-2' '/home/gpratt/projects/for_anthony/data/AV_stress_q331K_b_S18_L008_R2_001.fastq.gz'  '--stranded'  '--out-dir' '/projects/ps-yeolab2/for_anthony/analysis/av_mouse_stress_v1/AV_stress_q331K_b_S18_L008_R1_001.polyATrim.adapterTrim.rep.bamUnmapped.out.mate1.sailfish'  '--index' '/projects/ps-yeolab/genomes/mm9/sailfish'  '-n' 'AV_stress_q331K_b_S18_L008_R1_001.polyATrim.adapterTrim.rep.bamUnmapped.out.mate1.sailfish.sh'  '--out-sh' 'AV_stress_q331K_b_S18_L008_R1_001.polyATrim.adapterTrim.rep.bamUnmapped.out.mate1.sailfish.sh'  '-i' '/projects/ps-yeolab/genomes/mm9/sailfish' -p 16 --not-gzipped --do-not-submit && echo $(tail -n 2  'AV_stress_q331K_b_S18_L008_R1_001.polyATrim.adapterTrim.rep.bamUnmapped.out.mate1.sailfish.sh' ) | bash

Are we still using this script? If not I'll just remove it.

olgabot commented 8 years ago

Remove the script. Going to move to Kallisto in the near future

On Sat, Jan 9, 2016, 11:42 Gabriel Pratt notifications@github.com wrote:

Assigned #82 https://github.com/YeoLab/gscripts/issues/82 to @olgabot https://github.com/olgabot.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/82#event-510275491.

olgabot commented 8 years ago

Even sailfish authors say not to use 0.6.3 which is what we have

On Sat, Jan 9, 2016, 14:44 Olga Botvinnik obotvinn@ucsd.edu wrote:

Remove the script. Going to move to Kallisto in the near future

On Sat, Jan 9, 2016, 11:42 Gabriel Pratt notifications@github.com wrote:

Assigned #82 https://github.com/YeoLab/gscripts/issues/82 to @olgabot https://github.com/olgabot.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/82#event-510275491.