From the fastq data (read 1 and read 2) from illumina GAIIx platform ( paired-end library), I created the Sam and bam file using BWA. I got the statistics of number of uniquely-paired reads and total reads mapped to my reference genome. I was wondering how to get a complete list of insert size across the data set from my Sam or bam file? It could be just for uniquely paired reads or all mapped reads. I don't want to write a long script for that. Is there any easy commands from samtools or other options that I can use?
Question: Insert Size For Illumina Gaiix Paired-End Library From Sam/Bam File
7.4 years ago by
bioinfo • 740
bioinfo • 740 wrote:
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5 weeks ago by
Gabriel R. • 2.6k
Danmarks Tekniske Universitet
Gabriel R. • 2.6k wrote:
I have also a super simple program in C++ built on samtools/htslib to do just that:
It skips sec. alignments, QC fail. you can restrict the computation to mapped or properly paired for paired reads.
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