User: 27atcggcta27

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27atcggcta27160
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Posts by 27atcggcta27

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Comment: C: Has anyone here worked with CNCI before? EXHAUSTED
... oh man oh man oh man oh man you have given a beginner hope. Thank you! there was a problem with my twoBitToFa. Everything is working now after fixing. ...
written 9 months ago by 27atcggcta27160
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Comment: C: Has anyone here worked with CNCI before? EXHAUSTED
... Thank you Kevin for the advice, I was unable to find a CNCI tutorial so this is based purly off the github page. I am a newbie/beginner so if anyone knows of a tutorial I would appreciate the guidance. ...
written 9 months ago by 27atcggcta27160
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Comment: C: Has anyone here worked with CNCI before? EXHAUSTED
... Yes, I wanted to ask a formal question and this was more of just a forum post to just connect with others who have also used CNCI. I apologize if this violated etiquette. ...
written 9 months ago by 27atcggcta27160
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Comment: C: Has anyone here worked with CNCI before? EXHAUSTED
... Thank you. Yes, `twoBitToFa` is in my path. ...
written 9 months ago by 27atcggcta27160
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Has anyone here worked with CNCI before? EXHAUSTED
... Has anyone here worked with CNCI before? I'm just about exhausted trying to figure out what I'm doing wrong. So, I tried the following: python CNCI.py candidate_lncs.gtf -g -o test -m ve -p 16 -d ./dbase GRCm38.primary_assembly.genome.fa and I recieved the following error: name@server %5 ...
software error cnci forum rna-seq written 9 months ago by 27atcggcta27160 • updated 9 months ago by i.sudbery8.3k
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Answer: A: IGV crashing on Mac
... What version of Java are you using? IGV 2.4 and above requires at least Java version 8. You can chack here for other requirements https://software.broadinstitute.org/software/igv/ReleaseNotes/2.4.x ...
written 9 months ago by 27atcggcta27160
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Answer: A: How to check exon count of gene?
... Where did you get this gtf file? if it is a file you generated you may not have those exons ...
written 10 months ago by 27atcggcta27160
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Answer: A: Tophat Usage difficulty?
... here is a link to the manual for tophat [TOPHAT2 MANUAL][1] I highly suggest you use hisat2 over tophat though. It is a much better option. [1]: https://ccb.jhu.edu/software/tophat/manual.shtml ...
written 10 months ago by 27atcggcta27160
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Answer: A: How to Annotate Long non coding RNA?
... If I remember correctly, cuffmerge gives you a nonredundant list of transcripts between all your samples for you to use as the annotation later on. So I would apply the 200 nc cutoff here (merged.gtf) and then use CPAT. You could also use CNCI or CPC. ...
written 10 months ago by 27atcggcta27160
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Answer: A: How do I download mm10 major release genomic fasta and gtf file?
... As genomax pointed out you can get both from the gencode website. Just google gencode mouse and it should be the first hit (or just follow the link posted by genomax) for the GTF file, You will probably want the Comprehensive gene annotation for CHR region. just copy the link and use wget -c to do ...
written 10 months ago by 27atcggcta27160

Latest awards to 27atcggcta27

Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Has anyone here worked with CNCI before? EXHAUSTED
Scholar 9 months ago, created an answer that has been accepted. For A: How do I download mm10 major release genomic fasta and gtf file?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How do I download mm10 major release genomic fasta and gtf file?
Scholar 10 months ago, created an answer that has been accepted. For A: How do I download mm10 major release genomic fasta and gtf file?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How do I download mm10 major release genomic fasta and gtf file?

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