Hi all,
I have a bam file, and I would like to find the total number of reads (mapped + unmapped) from this file. I used the following command:
samtools idxstats myFile.bam
and received the following results:
chr1 248956422 15149505 0
chr2 242193529 5371045 0
chr3 198295559 5414053 0
chr4 190214555 2870332 0
chr5 181538259 7748857 0
chr6 170805979 6517305 0
chr7 159345973 7533417 0
chr8 145138636 3639326 0
It looks like the unmapped reads were removed. Is there any other way to find the initial number of reads from that bam file?
Thanks in advance:)
•
written
by
ilana.sychikov •
samtools view with option -c and the options -F and/or -f . Check the manual : http://www.htslib.org/doc/samtools.html
Thank you. I'm not sure I did it correctly, but I tried the following:
samtools view -F -c myFile.bam | wc
and received:
[main_samview] truncated file.
22389498 385093622 6170795057
Does it mean that there is a problem with my file?
no -F takes an argument (a bit set of sam flags ) . Please, read the manual.
-f int Only output alignments with all bits set in INT present in the FLAG field. INT can be specified in hex by beginning with
0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with0' (i.e. /^0[0-7]+/) [0].-F INT Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified in hex by beginning with
0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with0' (i.e. /^0[0-7]+/) [0].
Maybe you can find useful the samtools flagstat command. Here goes an example of the information it provides
samtools flagstat your_sam_or_bam.file
78413342 + 0 in total (QC-passed reads + QC-failed reads)
18152 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
600227 + 0 mapped (0.77%:-nan%)
78395190 + 0 paired in sequencing
39197595 + 0 read1
39197595 + 0 read2
471162 + 0 properly paired (0.60%:-nan%)
471162 + 0 with itself and mate mapped
117726 + 0 singletons (0.15%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
Thanks. It looks like there is no data regarding the unmapped reads in this BAM file.
This is the output of samtools flagstat command:
22389498 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
22389498 + 0 mapped (100.00%:-nan%)
22389498 + 0 paired in sequencing
11258030 + 0 read1
11131468 + 0 read2
21610733 + 0 properly paired (96.52%:-nan%)
21610733 + 0 with itself and mate mapped
778765 + 0 singletons (3.48%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
Am I right?
So there is no way to receive the initial number of reads from this file, correct?
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