User: CrisMar

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CrisMar70
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NYU
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Posts by CrisMar

<prev • 17 results • page 1 of 2 • next >
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Non Overlaps in bedtools intersect
... 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 ...
bedtools intersect iclip nonoverlaps written 3 months ago by CrisMar70 • updated 12 weeks ago by Biostar ♦♦ 20
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Answer: A: hg38 gtf file containing all RNAs and features
... 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 CrisMar70
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hg38 gtf file containing all RNAs and features
... 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 ...
gtf bedtools attributes annotations parser written 9 months ago by CrisMar70
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Answer: A: annotatePeaks.pl Homer using "RNA"
... Maybe this might help you: https://www.biostars.org/p/329227/ ...
written 10 months ago by CrisMar70
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Comment: C: Annotating bed files with Crosslinking induced truncations sites from iCLIP expe
... 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 CrisMar70
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Annotating bed files with Crosslinking induced truncations sites from iCLIP experiment (chromosome locations).
... 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 ...
bedtools cits intersect iclip annotate written 10 months ago by CrisMar70 • updated 10 months ago by Pierre Lindenbaum120k
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Comment: C: Annotate .bed file with gene names
... 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 CrisMar70
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Answer: A: Math-CDF Perl Module compiler issue
... 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 CrisMar70
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Comment: A: Math-CDF Perl Module compiler issue
... 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 CrisMar70
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Math-CDF Perl Module compiler issue
... 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 ...
perl compiler perl module gcc written 10 months ago by CrisMar70

Latest awards to CrisMar

Popular Question 8 months ago, created a question with more than 1,000 views. For RIPSeeker Bioconductor package, insights?
Scholar 10 months ago, created an answer that has been accepted. For A: Math-CDF Perl Module compiler issue
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: RIPSeeker Bioconductor package, insights?

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