User: CrisMar
CrisMar • 70
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- NYU
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- Email:
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Posts by CrisMar
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... I have a bed file from an iCLIP experiment that I needed to annotate (i.e. identify the genes) where the crosslinks are predicted.
I used bedtools intersect to annotate my crosslinks (i.e. the bed file) to the human gtf file (same one used for mapping/alignments) with parameters that would output ...
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... Yes, I have this bed file:
$head CITS.bed
chr1 568974 568975 CITS_1[gene=chr1_f_c24][PH=12][PH0=0.29][P=1.01e-12] 12 +
chr1 2239149 2239150 CITS_2[gene=chr1_f_c1136][PH=7][PH0=0.40][P=2.21e-04] 7 +
chr1 2239899 2239900 CITS_3[gene=chr1_f_c1138][PH=6][PH0=0.21 ...
written 9 months ago by
CrisMar • 70
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... Hi All,
I annotated a bed file with an hg38 gtf file (from gencode) using bedtools intersect.
https://www.biostars.org/p/329227/
Although it worked well the attributes column in the hg38 file is a mess.
1. Trying to separate each attribute in one column with the corresponding attribute turned out ...
written 9 months ago by
CrisMar • 70
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... Maybe this might help you: https://www.biostars.org/p/329227/ ...
written 10 months ago by
CrisMar • 70
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... Ok that makes more sense now! I tried using those options but not together. Thanks! The file has everything I need now! ...
written 10 months ago by
CrisMar • 70
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... Hello,
I have a bed file listing chromosome regions corresponding to CITS (crosslink induced truncation sites), thus one nucleotide listed below. These sites are from an iCLIP experiment to identify binding sites of a specific RNA-binding protein.
$head CITS.bed
chr1 568974 568975 CITS ...
written 10 months ago by
CrisMar • 70
• updated
10 months ago by
Pierre Lindenbaum ♦ 120k
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... If you separated gtf and bed files for each strand (+ and -) is there a way to merge the resulting files together?
Also what is there are multiple features that match your new_file? I am interested in also getting 'exon, intron, 3'UTR, 5'UTR' features too. ...
written 10 months ago by
CrisMar • 70
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... Can't seem to delete the post, but thanks everyone for your help. The solution here was just to delete the -'-no-cpp-precomp' flag from the makefile and re run. It is running smoothly now, I am using it for this bioinformatics protocol:
https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation ...
written 10 months ago by
CrisMar • 70
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... Thanks! I am still new at this, will move it over to stack over flow soon.
Will try CPAN minus as soon as I get to a better connection.
Only using ActivePerl because I was told to have the latest version, but I see your point, hope all these issues get sorted out.
...
written 10 months ago by
CrisMar • 70
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... Hello,
Cannot find the answer anywhere online. Trying to compile a Perl Module, Math-CDF, for an CLIP (RNA-protein crosslink analysis) and I am getting an error when I run the make commands.
Within the folder I have to run:
$perl Makefile.PL
$make
$make test
$make install
running ...
written 10 months ago by
CrisMar • 70
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