User: montoya.oscar

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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.oscar50
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Answer: A: cutadapt loop and paired-end reads
... 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.oscar50
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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.oscar50
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Answer: A: How to deal with demultiplexed Miseq pair-end (2*250bp) 16S data using QIIME?
... 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.oscar50

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Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Pathway Analysis In R

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