User: kevt1999

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kevt19990
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Posts by kevt1999

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Comment: C: Peak calling on FastX-collapser processed data
... You are right, I am doing an RNA-IP, which involves fragmenting total RNA and pulling down RNA with an antibody targeting methylated RNA. I posted in the ChIP-seq section because my analysis pipeline is closer to ChIP-seq then RNA-seq. Yes, I'll do fastqc on the data after index trimming.   ...
written 4.0 years ago by kevt19990
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Comment: C: Peak calling on FastX-collapser processed data
... Thank you for the reply! By "do not see much to be gained", do you mean I should not worry about CPU cycles, and feed the fully duplicated data set though Bowtie and then MACS? I see I have about 1-10 million duplicates for each read. ...
written 4.0 years ago by kevt19990
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Peak calling on FastX-collapser processed data
... I am processing IP data by first aligning with Bowtie then doing peak calling with MACS. To save CPU cycles, I was told that I should use the FastX-collapser tool ( http://hannonlab.cshl.edu/fastx_toolkit/ ) to remove duplicate reads before feeding my reads into Bowtie. The collaper tool takes fasta ...
chip-seq written 4.0 years ago by kevt19990 • updated 4.0 years ago by Ian5.5k

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