User: robbenstijn

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Posts by robbenstijn

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Selecting relevant binding sites according to MACS data
... I've got ChIP-seq data analyzed with MACS and looks at such: > chr start end length summit tags -10log10(pvalue) fold_enrichment FDR(%) > chr1 9911 10616 706 251 77 60.46 4.07 0.30 > chr1 11119 11740 622 185 32 101.80 10.0 ...
macs peaks analysis written 19 months ago by robbenstijn0 • updated 18 months ago by le233660
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Comment: C: Determine promoter regions relative to TSS.
... That's great, thanks! Would you happen to have this piece of literature so I can validate my actions? I tried finding it myself but wasn't able to. ...
written 19 months ago by robbenstijn0
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Determine promoter regions relative to TSS.
... I'm trying to determine a general region for a promoter relative to a TSS. I've got data of MAC peaks and their locations and I'd like to check whether these MAC peaks appear somewhere on a promoter region. Therefore I need to determine general a rule of thumb for the promoter region relative to t ...
upstream promoter downstream tss written 19 months ago by robbenstijn0 • updated 19 months ago by bharata1803290
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Comment: C: BAM to BIGWIG
... I did just that and it worked. Now I get another error, would you happen to know what it means? Thanks! Traceback (most recent call last): File "BAM_BIGWIG.py", line 136, in main(*args, **kwargs) File "BAM_BIGWIG.py", line 62, in main convert_to_bigwig(wig_file, chr ...
written 19 months ago by robbenstijn0 • updated 19 months ago by genomax56k
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Comment: C: BAM to BIGWIG
... Yes about that, do you know how to install this? What I did was that i went to this link: http://hgdownload.cse.ucsc.edu/admin/exe/ Clicked on macOSX.i386/ Clicked on wigToBigWig And then this file started to download. But I'll probably need to install it right? Now I posted it in the same director ...
written 19 months ago by robbenstijn0
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Comment: C: BAM to BIGWIG
... I renamed the bam_to_wiggle.py file from the link above to BAM_BIGWIG.py. Does this answer your question? Thanks for your help btw! ...
written 19 months ago by robbenstijn0
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Comment: C: BAM to BIGWIG
... I tried this, but when I run: python BAM_BIGWIG.py Galaxy6RmDupdata.bam (Galaxy6RmDupdata.bam is the name of my bam file) I get: Traceback (most recent call last): File "BAM_BIGWIG.py", line 136, in main(*args, **kwargs) File "BAM_BIGWIG.py", line 62, in main ...
written 19 months ago by robbenstijn0 • updated 19 months ago by WouterDeCoster32k
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BAM to BIGWIG
... I'm trying to convert a BAM file to a BIGWIG file on my mac using the following link: https://github.com/chapmanb/bcbb/blo...m_to_wiggle.py Could someone explain what commands I have to put into the terminal (or in Sublime Text)? My BAM file is called Galaxy6RmDupdata.bam. I couldn't figure this o ...
bioinformatics github bam bigwig terminal written 19 months ago by robbenstijn0 • updated 19 months ago by EagleEye5.7k

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