User Activity
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Posted
a comment
on
discussion General Discussion
on
APAtrap
Hi Hugo, Our APAtrap pipeline does not currently support parallel computing. One way to speed up the process is, as you mentioned, to separate bedgraph files and gene model file based on their genomic positions, and process them separately and/or simultaneously. Since the result for each gene corresponds to only one line in the output file, you can use the "cat" command line tool to combine them. Best, Congting
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Posted
a comment
on
discussion General Discussion
on
APAtrap
Hi Marie, It's clear that you used an incorrect gene model file, the gene model file should be in bed12 format. You could go to this link http://genome.ucsc.edu/FAQ/FAQformat#format1manual for details, and go to the user manual page to see how to make a suitble gene model file from GTF file of genome annotation. Congting Ye
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Modified
a wiki page
on
QuantifyPoly(A)
User Manual
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Modified
a wiki page
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scDAPA
User Manual
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Modified
a wiki page
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scDAPA
User Manual
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Modified
a wiki page
on
scDAPA
User Manual
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Posted
a comment
on
discussion General Discussion
on
APAtrap
Hi Andrew, It would be better that you could send me the ICF.APA.txt file for figuring out the problem. Congting
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Modified
a wiki page
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QuantifyPoly(A)
User Manual
Personal Data
- Username:
- yec
- Joined:
- 2014-05-11 16:37:17
- Location:
- Xiamen / China / CST
- Gender:
- Male
Projects
This is a list of open source software projects that Congting Ye is associated with:
- APAtrap Identification of APA sites from RNA-seq data Last Updated:
- QuantifyPoly(A) Quantification of poly(A) sites from 3' end sequencing data Last Updated:
- detectIR Detection of Perfect and Imperfect Inverted Repeats Last Updated:
- detectMITE Detection of Miniature Inverted Repeat Transposable Elements Last Updated:
- scDAPA Detection and visualization of dynamic alternative polyadenylation Last Updated: