HI all, I have paired reads, for & rev of 150 bp.
I used the picard tools to estimate insert size.
The output file has median size for both for & reverse with different sizes,
MEDIAN_INSERT_SIZE
185 ... FR
133 ... RF
my understanding is that Mean Inner Distance between Mate Pairs is: mode - 2*read length.
In this case however which number should I use? the FR or RF since they give very different results.
- I used tophat2 to generate the bam file first then I used picard with the following commands,
java -Xmx2g -jar pathtopicard\CollectInsertSizeMetrics.jar INPUT=accepted_hits.bam OUTPUT=size.txt
Thanks.
I used the picard tools to estimate insert size.
The output file has median size for both for & reverse with different sizes,
MEDIAN_INSERT_SIZE
185 ... FR
133 ... RF
my understanding is that Mean Inner Distance between Mate Pairs is: mode - 2*read length.
In this case however which number should I use? the FR or RF since they give very different results.
- I used tophat2 to generate the bam file first then I used picard with the following commands,
java -Xmx2g -jar pathtopicard\CollectInsertSizeMetrics.jar INPUT=accepted_hits.bam OUTPUT=size.txt
Thanks.
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