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bioinfo-biols / CIRIquant

circular RNA quantification tools
https://sourceforge.net/projects/ciri/files/CIRIquant
MIT License
27 stars 18 forks source link

Add support for strand specific RNA-seq data #3

Closed Kevinzjy closed 4 years ago

DarioS commented 4 years ago

Stranded protocol is more common these days than unstranded protocol, so I hope you add it soon.

Kevinzjy commented 4 years ago

Hi @DarioS , I added the options for stranded library in the new beta branch, but I don't have any stranded RNA-seq data at hand. Could you try this version on your data to see how it's working?

Kevinzjy commented 4 years ago

Also fixed #7 #8

DarioS commented 4 years ago

I don't know what to look for in the results to judge if they are good or bad. ENCODE Project has many freely available strand-specific RNA sequencing files to download. You could try using GM12878 R1 and GM12878 R2 FASTQ files. You can click the purple Download button on the webpage to get a FASTQ file.

Kevinzjy commented 4 years ago

Thanks, I'm testing on it.

Kevinzjy commented 4 years ago

Hi @DarioS , support for stranded library and GFF3 format annotation (#9) was added in the latest version 1.1 .