Extract information of mapped reads bam files
Hi all, I have a bam files from RRBS data and want to extract these information from them, anyone know how I can get these output (an example is below)?
Thanks in advance,
Output
20000 reads; of these:
20000 (100.00%) were unpaired; of these:
1247 (6.24%) aligned 0 times
18739 (93.69%) aligned exactly 1 time
14 (0.07%) aligned >1 times
93.77% overall alignment rate
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2 answers
You can use samtools for this. Please check out in this link.
samtools flagstat RRBS_data.bam
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No tool produces the exact same stats that you'd get when running the aligner (the output looks to be generated by bowtie )
But there are alternative tools designed to produce stats, for example bamstats
https://github.com/guigolab/bamstats
an output could look like this:
{
"general": {
"protocol": "SingleEnd",
"reads": {
"total": 101567,
"unmapped": 7119,
"mapped": {
"0": 94448
},
"mappings": {
"ratio": 1,
"count": 94448
}
},
"pairs": {}
}
}
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