http://seqanswers.com/forums/showthread.php?t=8190
https://www.biostars.org/p/110289/
http://seqanswers.com/forums/showthread.php?t=29975
Here are few tips I found necessary to share in order to have it work:
For example, if you want to exclude all reads mapped to human mitochondrial genome, you can use
echo "chrM 0 16571 mt 0 ." | bedToGenePred stdin stdout | genePredToGtf file stdin chrM.gtf
2. "-M" option also works for de novo assembly (cufflinks -g).
3. Using "-M" option should theoretically increase the FPKM value (comparing to no mask). So, if you observed opposite tread, there must be something wrong.
4. If you expect a lot of reads from the mask regions (e.g. chrM, rRNAs), you can substract the masked reads from your bam file before feeding to cufflinks, for example using "samtools view -L retained_region.bed".
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