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Old 09-12-2015, 05:01 AM   #21
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 807

Convert your BAM file to FASTQ, then use Kallisto.

The crazy thing is that this might actually be quicker than other methods.
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Old 09-14-2015, 06:26 AM   #22
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Originally Posted by dpryan View Post
There are some entries that htseq-count will skip (those without exons?), which presumably is why this happens. Anyway, you need to ensure that everything is in the same order anyway, so make sure to write meaningful row names and use those with match().
Thank you D. Very helpful.
And I also found Cufflinks could calculate RPKM directly.
cufflinks -o OutDir -g hg19/genes.gtf TopHat/accepted_hits.bam
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Old 11-01-2016, 06:50 AM   #23
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So the script worked for me and I got an mm9.fa.fai file as output, wondering how this can be used with edgeR to generate the RPKMs? Thanks.
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bam, htseq-count, rna-seq, rpkm, tpm

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