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Old 08-30-2013, 07:55 PM   #1
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Join Date: Aug 2013
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Post Low mapping rate for RNAseq 2x150 trimmed data

I just got a data set from my collaborator. 2 X 150 bps, Illumina RNAseq data for human samples. We did QC on the data and trimmed it to remove adaptors and low quality bases. Then I use tophat2 to map them to hg19 in three ways:

1. paired end mapping with default parameters;
2. single end mapping for each end separately;
3. paired end mapping with inner distance between the two ends to have a mean of 0 and sd=50;

Mapping rate for 1 and 3 are both around 45%. But mapping rate for 2 is around 75%. So most of the reads are mappable but cannot be paired even when the inner distance between the two ends can be 0 or negative (if the distance can go negative). I took a look at the BAM files for the accepted hits. It looks like read pairs with alignment


can be paired. But read pairs with alignment


can not be paired. Does any one know why and how I can gain those unpaired alignment back? Thanks in advance!
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rnaseq low mapping rate

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