Moderator: ATpoint

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ATpoint7.4k
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#! /usr/bin/Rscript

class(ATpoint)

> [1] 50% wet-lab rat

> [2] 50% wannaba computational biologist


cat(Research_Interests)

> Impact of somatic mutations on the non-coding genome

Posts by ATpoint

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Comment: C: GRCh37.p13 download at NCBI FTP?
... Yes Ma'am. Apologies for my carelessness ;-) ...
written 5 hours ago by ATpoint7.4k
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Answer: A: Desegregation of animals and locations
... Assuming `"\t"` between columns and `whitespace` between animals, do: while read p; do grep $p your_list.txt | cut -f1 | cat <(echo $p) <(cat /dev/stdin); done < <(cut -f2 your_list.txt | awk 'NR > 1 {gsub(" ", "\n"); print $0}' | awk NF | sort -k1,1 -u) It takes the unique IDs ...
written 5 hours ago by ATpoint7.4k
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Comment: C: Desegregation of animals and locations
... What are the delimiters between the columns (I assume tab) and between the animals (I assume whitespace)? ...
written 5 hours ago by ATpoint7.4k
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Comment: C: Desegregation of animals and locations
... Hello hosein_salehi6! Please do not post duplicates. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, we'll be happy to talk about it. Cheers! ...
written 5 hours ago by ATpoint7.4k
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Comment: C: GRCh37.p13 download at NCBI FTP?
... You can get it [from Ensembl][1] ensemble =), downloading `Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz`. Still GRCh19 is old. Any reason you do not go with GRCh38? [1]: ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/ ...
written 6 hours ago by ATpoint7.4k
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Comment: C: Parsing header of FASTA File
... Did it work for you @Shelle ? ...
written 7 hours ago by ATpoint7.4k
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Comment: C: How different is rlog transformation from vst transformation in DESeq2
... Did you read this one already: [Question: Is there a conceptual difference between vst/rlog transforms and lfcShrink?][1]? [1]: https://support.bioconductor.org/p/104615/ ...
written 7 hours ago by ATpoint7.4k
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Comment: C: 1d fetures and 2d features of a protien
... Hi kgma225, please reformat your question. There are multiple typos and a lack of details and content, as Ram already mentioned. Both might make you look lazy, demotivating people to help you. Putting some effort into your question will notably increase your chance of an elaborate answer. ...
written 22 hours ago by ATpoint7.4k
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Comment: C: hisat2 / bowtie: read has more quality values than read characters
... Are you pipe the output into a sorting tool that might take up some memory? ...
written 1 day ago by ATpoint7.4k
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Comment: C: FRIP score ATAC-seq
... Good catch with the switched `-a/b`, didn't even notice that :) ...
written 1 day ago by ATpoint7.4k

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