User: Melonhead

gravatar for Melonhead
Melonhead10
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4 months ago
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5 months ago
Email:
a***************@gmail.com

Posts by Melonhead

<prev • 7 results • page 1 of 1 • next >
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Comment: C: htseq-count cannot locate gff
... To be honest, I've never used any of these before :^) I will gladly try different approach. Thank you for the suggestion! ...
written 4 months ago by Melonhead10
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Comment: C: htseq-count cannot locate gff
... Oh yes, now I see a mistake. I mislabeled the function in for loop Thank you! ...
written 4 months ago by Melonhead10
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Comment: C: htseq-count cannot locate gff
... The output of cat -A HTseq_count_int.sh : #!/usr/bin/bash$ $ #Script to convert .BAM to .SAM and quantify gene expression with HTseq$ $ #Get WD$ currentdir=$(cd -P -- "$(dirname -- "$0")" && pwd -P)$ wd=$(dirname $currentdir)$ wdsamp="Analysis/Samples"$ $ ...
written 4 months ago by Melonhead10
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Comment: C: htseq-count cannot locate gff
... It should be: -rw-r--r-- 1 1,4K May 29 14:49 HTseq_count_int.log -rw-r--r-- 1 1,6K May 29 14:49 HTseq_count_int.sh -rw-r--r-- 1 70M May 29 14:49 Rattus_norvegicus.Rnor_6.0.96.dexseq.int.gff I also tried providing the absolute path to the .gff. Still of no avail. ...
written 4 months ago by Melonhead10
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htseq-count cannot locate gff
... Hi there I am struggling with the trivial task of running htseq-count. My command is as follows: htseq-count -r pos \ -s no \ -t exonic_part \ -i transcripts \ --additional-attr=gene_id \ -m union \ --nonunique=all \ -f sam \ Analysis/Samples/sam/"${prefix}_Map ...
alignment rna-seq written 4 months ago by Melonhead10
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Comment: C: bowtie2 alignment to rRNA, ERCC spike ins, Repetitive Elements and index creatio
... Apologies, will do next time Thank you ...
written 5 months ago by Melonhead10
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bowtie2 alignment to rRNA, ERCC spike ins, Repetitive Elements and index creation
... I have downloaded .fastqfiles from SRA and now trying to filter out reads aligning to ERCC spike ins, rRNA and Repetitive Elements (from RepeatMasker). I would like to do this step by step, repeating the command on the unaligned results from the previous step using something like this: bowtie2 ...
alignment rna-seq written 5 months ago by Melonhead10 • updated 3 months ago by Biostar ♦♦ 20

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