Question: Skip orientation RF
0
gravatar for Folder40g
3.9 years ago by
Folder40g120
Folder40g120 wrote:

Hi, I'm using BWA to align some exome sequences:

/home/Programas/bwa-0.7.10/bwa index -p genome -a bwtsw /local/Referencias/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.7.10-r789/genome.fa

/home/Programas/bwa-0.7.10/bwa mem -t 10 /local/Referencias/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.7.10-r789/genome /local/CLL/Raw_data/MONONUCLEARCells_R1.fastq.gz /local/CLL/Raw_data/MONONUCLEARCells_R2.fastq.gz > /local/CLL/Processing/FGO/Alignment/FGO_20070115_MONONUCLEARCells.sam

 

These are the "warnings" shown by bwa.

[M::main_mem] read 1315790 sequences (100000040 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (65, 570757, 14, 19)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (80, 109, 176)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 368)
[M::mem_pestat] mean and std.dev: (127.23, 64.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 464)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (166, 200, 248)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (2, 412)
[M::mem_pestat] mean and std.dev: (210.69, 60.88)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 494)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (79, 194, 389)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1009)
[M::mem_pestat] mean and std.dev: (242.92, 225.64)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1319)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (104, 150, 224)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 464)
[M::mem_pestat] mean and std.dev: (157.95, 63.90)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 584)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR

 

And

[M::mem_pestat] low and high boundaries for proper pairs: (1, 499)
[M::mem_pestat] skip orientation RF as there are not enough pairs

 

Should I be worried (about the skip orientation...). This is the first time I have seen this output.

 

Thanks one more time.

orientation skip bwa rf exome • 2.9k views
ADD COMMENTlink modified 3.1 years ago by wzchang0 • written 3.9 years ago by Folder40g120
0
gravatar for Devon Ryan
3.9 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

Unless you have mate pairs, they shouldn't face away from each other (aka, have an RF orientation). This is expected with illumina sequencing.

ADD COMMENTlink written 3.9 years ago by Devon Ryan93k

I do have illumina data.

ADD REPLYlink written 3.9 years ago by Folder40g120
0
gravatar for wzchang
3.1 years ago by
wzchang0
wzchang0 wrote:

This is normal. The Illumina reads orientation is FR. You got majority FR and skipped other three.

ADD COMMENTlink written 3.1 years ago by wzchang0

If there is an inversion, might that be interpreted by the aligner as, say, FF orientation, and should therefore be included in SAM/BAM rather than being skipped?

ADD REPLYlink written 5 months ago by bdolin90
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