User: Grinch

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Grinch0
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Posts by Grinch

<prev • 11 results • page 1 of 2 • next >
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Answer: A: database for enhancer sequences in human/mammal genomes
... There are many databases available: EnhancerAtlas: http://enhanceratlas.org/, VISTA https://enhancer.lbl.gov/, FANTOM http://fantom.gsc.riken.jp/5/data/, DenDB: http://www.cbrc.kaust.edu.sa/dendb/ ...
written 3 months ago by Grinch0
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Answer: A: fastQC - case of the anomalous last base
... Hi, my first thought is, was your sample treated in any way or do you have any overrepresented sequences? If the bias is only at the final base, than it's most probably due to too aggressive adapter trimming, or due to your trimming of final bases. How long are your reads? Is it paired-end? There ...
written 3 months ago by Grinch0
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Answer: A: Merge three assembled files (iterations) into one.
... This is an old question, but it might be useful for someone else with the same question. For StringTie merge, you need to merge all the samples, regardless if you have treated/untreated or healthy/cancer samples. What it does is, it makes a sort of reference GTF file with all the expressed transcrip ...
written 3 months ago by Grinch0
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Comment: C: How To Sort Sam File
... sort: invalid option -- 'O' sort: invalid option -- 'T' This is the error I get if I try this command. I don't see -O and -T flags in the man pages on SamTools. From where you got this flags? ...
written 6 months ago by Grinch0
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MeDIP-seq and hMeDIP-seq analysis
... Hi! I'm analysing MeDIP-seq and hMeDIP-seq data for the first time (I've analysed ChIP-seq and RNA-seq data sets before) and was wondering if people who have done it before can recommend pipelines they have used and/or programmes for quantitative comparison of ChIP-Seq data. My data set is made of r ...
medip-seq hmedip-seq chip-seq written 16 months ago by Grinch0 • updated 16 months ago by dally140
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How to remove illumina PCR primer 2.01 from RNA-seq samples
... I have RNA-seq samples that are highly contaminated with Illumina PCR primer 2.01, which programme is best to use to remove those?     ...
illumina rna-seq written 19 months ago by Grinch0 • updated 19 months ago by Juke-34960
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Comment: C: Change column content with shell scripting
... It's an ''annotation file for ChIP-seq peaks'' that i need help with. I just put random names to the files because i though it wasn't important. ...
written 21 months ago by Grinch0
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Comment: C: Change column content with shell scripting
... The problem is these words appear in other columns as well, but i don't want to change those, so just the ones in column 17. ...
written 21 months ago by Grinch0
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(Closed) Change column content with shell scripting
... Here is my problem; I have a spreedsheet (.txt) with 20 columns, for one column named ''xyz'' I want to change its content so if there is for example: aaa or bbb or ccc in the column field - I want to change it to ABC; if the field contains KFL or TST - i want to change it to KTTS etc. How can I do ...
shell scripting spreedsheet written 21 months ago by Grinch0 • updated 21 months ago by Assa Yeroslaviz1.1k
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Comment: C: Generating the output file name from the input file in bash script
... Thank you! That saved so much time :) ...
written 24 months ago by Grinch0

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Popular Question 15 months ago, created a question with more than 1,000 views. For Generating the output file name from the input file in bash script

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