User: DVA
DVA • 430
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Posts by DVA
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Comment:
C: Mask gtf file for cufflinks
... Do you know if my library is 3' rna seq library, what parameters should I alter with StringTie? Ideally, for 3' rna seq lib, transcript assembly is not needed for our DE analysis. Some default setting such as 200bps in -m, minimum length allowed for predicted transcripts，will be not relevant.
What ...
written 10 days ago by
DVA • 430
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Comment:
C: Mask gtf file for cufflinks
... Yes absolutely. That is what I will do next. Thank you! ...
written 11 days ago by
DVA • 430
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C: Mask gtf file for cufflinks
... Thanks a lot. I was trying to repeat a previous analysis done by a colleague. ...
written 11 days ago by
DVA • 430
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... Is the ["-M" option][1] necessary when using Cufflinks? I understand it would prevent downstream analysis focusing on regions like rRNA, but could this be done at the very end after differential expression? Also, I could not find a mask gtf to download from USCS genome browser... Any advice please? ...
written 11 days ago by
DVA • 430
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... Wooo thank you! This is of great help! ...
written 25 days ago by
DVA • 430
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... I am new to HISAT2 and trying to play around with its options. I found the following issues and would appreciate your advice:
1. I downloaded the genome_tran (for grch38) folder, and wanted to check out the option: --tmo. According to the [manual][1], it should "Report only those alignments within ...
written 25 days ago by
DVA • 430
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... okay will do. Thank you for all the comments you provided to my questions recently. ...
written 6 weeks ago by
DVA • 430
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... In my poly A capture RNA sequencing fastq output, I noticed that about 20% of the reads contain poly A in the middle (or even close to the front). I would like to understand more on this, because with DNA fragments mostly >300bps and read length 100 bps, we were not expecting to see poly A show u ...
written 6 weeks ago by
DVA • 430
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... Thank you for the confirmation! ...
written 6 weeks ago by
DVA • 430
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... I thought the adaptor is always showing up at the left of the reads... why they will not be at the same spot please?
Sorry for all these questions, but I really want to understand it better. Thank you. ...
written 6 weeks ago by
DVA • 430
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For Non-cancer somatic mutation calling
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For Remove both pair end reads with low mapping quality using Samtools
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For Remove both pair end reads with low mapping quality using Samtools
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For Non-cancer somatic mutation calling
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For Remove both pair end reads with low mapping quality using Samtools
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For A: Can't locate dbSNP 131 anymore?
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For A: Can't locate dbSNP 131 anymore?
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