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Recent Replies
Comment: How to download all the Zn-binding protein sequences from MetalPDB?
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GenoMax
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There is a [flat database available][1] on the site you linked above. It appears to be in XML format so you will need to likely parse that …
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ATpoint
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Shouldn't you assess transcription by an actual RNA-based assaay such as CAGE or RNA-seq rather than guessing based on PolII?
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Sure. I've been meaning to create a how-to on the super/subscript formatting. For super-script, you can use the `<sup> ... </sup>` HTML ele…
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You should be able to use pipes to string those steps together
samtools view -f 12 -F 256 aligned-sorted-deduplicated.bam | samtools s…
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I know this is an old thread but if anyone has the same problem I prefer to write it here because it is one of the first results in google.…
Comment: how to select peaks at not transcribed genes
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Lila M
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That is my concern... this is why I asked in here :)
Comment: how to select peaks at not transcribed genes
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jared.andrews07
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In that case, wouldn't you consider all peaks to be associated with transcription? Even if your 232 peaks are not associated with genes, th…
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Try the following.
seqkit fx2tab --name --only-id --gc contigs.fa | awk -F "\t" '{if ($2 < 35) print $1}' | xargs -n 1 sh -c 'seqki…
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...besides, [wget](https://www.gnu.org/software/wget/manual/wget.html) has a `-c/--continue` option to resume the download of a partial fil…
Comment: how to select peaks at not transcribed genes
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jared.andrews07
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What makes you think genes with a peak are transcribed while those without are not? Unless your IP was for Pol2, this is an overly simplist…
Comment: How to combine 2 incomplete GTF
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Thank you! I am going to try it :)
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Please create a new environment when installing packages. That avoids conflicts.
conda create -c bioconda -n agat agat
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Comment: How to combine 2 incomplete GTF
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Hi Juke,
I am trying to install it and I can't.
![enter image description here][1]
[1]: /media/images/bc08978b-10f7-4666-b385-57807b…
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I agree with you, Mensur, that the GTDB is arguably more reliable and comprehensive than NCBI. However, due to the relative greater longevi…
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