Hi all,
I am having some issues interpreting the output from the bamtools stats command. I am working with paired end RNAseq data generated from olive baboon vaginal swabs (so we are expecting some bacterial contamination). I mapped the sequences to the olive baboon reference genome using STAR, and then used the bamtools stats command to see how many reads are mapping. The output is a bit perplexing because the samples consistently have a much higher proportion of forward strand reads than reverse strand reads, while the number of R1 reads is equal to the number of R2 reads. I have pasted the output of one file below:
**********************************************
Stats for BAM file(s):
**********************************************
Total reads: 30135821
Mapped reads: 1274337 (4.22865%)
Forward strand: 29498803 (97.8862%)
Reverse strand: 637018 (2.11382%)
Failed QC: 0 (0%)
Duplicates: 0 (0%)
Paired-end reads: 30135821 (100%)
'Proper-pairs': 1272676 (4.22313%)
Both pairs mapped: 1272676 (4.22313%)
Read 1: 15067605
Read 2: 15068216
Singletons: 1661 (0.00551171%)
Does anyone have any ideas of what might be going on here? I've looked at the raw reads and there are approximately the same number of reads in the R1 and the R2 files.
Thank you in advance for your advice!
I am having some issues interpreting the output from the bamtools stats command. I am working with paired end RNAseq data generated from olive baboon vaginal swabs (so we are expecting some bacterial contamination). I mapped the sequences to the olive baboon reference genome using STAR, and then used the bamtools stats command to see how many reads are mapping. The output is a bit perplexing because the samples consistently have a much higher proportion of forward strand reads than reverse strand reads, while the number of R1 reads is equal to the number of R2 reads. I have pasted the output of one file below:
**********************************************
Stats for BAM file(s):
**********************************************
Total reads: 30135821
Mapped reads: 1274337 (4.22865%)
Forward strand: 29498803 (97.8862%)
Reverse strand: 637018 (2.11382%)
Failed QC: 0 (0%)
Duplicates: 0 (0%)
Paired-end reads: 30135821 (100%)
'Proper-pairs': 1272676 (4.22313%)
Both pairs mapped: 1272676 (4.22313%)
Read 1: 15067605
Read 2: 15068216
Singletons: 1661 (0.00551171%)
Does anyone have any ideas of what might be going on here? I've looked at the raw reads and there are approximately the same number of reads in the R1 and the R2 files.
Thank you in advance for your advice!
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