User: montoya.oscar
montoya.oscar • 50
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Posts by montoya.oscar
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Answer:
A: STAR outputs empty alignment
... I encountered a similar (or same) problem where the output files from STAR contained only zeros. It was solved by converting the **.gff** file into **.gtf**. Use `gffread -E annotation.gtf -o-` to generate a **.gtf**. [See http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread][1] under **The gffre ...
written 8 months ago by
montoya.oscar • 50
1
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2
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5.2k
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2
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... Based on h.mod's hint, the following code removes three pairs of primers (three forward and thre reverse) and their reverse complements (simply the same primers sequences but backwards):
for i in *_R1_001.fastq.gz
do
SAMPLE=$(echo ${i} | sed "s/_R1_\001\.fastq\.gz//")
echo ${SA ...
written 3.0 years ago by
montoya.oscar • 50
3
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7
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29k
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7
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Answer:
A: Pathway Analysis In R
... Take a look at clusterProfiler, DOSE, and STRINGdb packages, all in Bioconductor. ...
written 3.9 years ago by
montoya.oscar • 50
1
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4
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15k
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4
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... Hi all,
I know this's an old question, but many people face this same mapping file issue fairly often. This is a link to QIIME's support site explaining how to deal with Illumina paired-end output (only to extend nkuyfq answer):
http://qiime.org/tutorials/processing_illumina_data.html ...
written 4.8 years ago by
montoya.oscar • 50
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