In your analysis of RNA-Seq pipeline, which of the following steps do you normally do?
(Illumina)
PRE-PROCESSING
1) removal of reads with consecutive stretches of "B" qualities
2) trimming 3' end (what criteria do you use?)
3) trimming 5' end (what criteria do you use?)
4) removal of duplicate reads (reads that start at the same exact position, both in first and second mate)
Diff Exp ANALYSIS
5) Removal of strand assignment before estimating abindances
6) tophat/cufflinks/cuffdiff
7) bowtie and DESeq/EdgeR/DEGSeq
ENRICHMENT
8) correction length bias (goseq)
9) ....
Thanks!
(Illumina)
PRE-PROCESSING
1) removal of reads with consecutive stretches of "B" qualities
2) trimming 3' end (what criteria do you use?)
3) trimming 5' end (what criteria do you use?)
4) removal of duplicate reads (reads that start at the same exact position, both in first and second mate)
Diff Exp ANALYSIS
5) Removal of strand assignment before estimating abindances
6) tophat/cufflinks/cuffdiff
7) bowtie and DESeq/EdgeR/DEGSeq
ENRICHMENT
8) correction length bias (goseq)
9) ....
Thanks!
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