hi!
i am confused when to use TopHat "-M/--prefilter-multihits and when not
"When mapping reads on the transcriptome,...
6 results in 0.0023 seconds.
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TopHat -M/--prefilter-multihits; unmapped reads
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How to assign reads with multiple mapped locations for RNA-Seq quantification
Hello all,
I might be missing other threads about this here. But in terms of generating expression profiles from RNA-Seq data, I am wondering... -
Gene expression of duplicate genes
I have some polyA(minus) RNAseq data and would like to quantify the gene expression of Pol3 transcribed genes. Well, quite a lot of these are duplicate... -
edgeR/DESeq and multi-mapping reads
I have a RNAseq data-set with the majority (90%) of the reads being multi-reads (multi-hits / multi-mapped reads). The data is from sperm, so the high... -
Bowtie XA, X0, X1 tags in SAM output
Hi Everyone,
Background: I've been using bowtie and samtools for a couple years. In the past 6 months have I converted to outputing SAM... -
retain multihit reads for CNV analysis
Dear all,
My next question may have already been addressed so please forgive me if it was.
...
