BWA infered external isize ?

[crotoc]

hello,everyone. I am a newer to Chip-seq analysis and have a question about BWA. I analyzed my paired-end data with BWA and wanted to use MACS when doing peak calling. I have asked the authors of MACS about the input format for paired-end read, and he answered me as following:
"The implementation of SAM/BAM support follows the
previous ELANDMULTIPET implementation, hence fragments are extended
according to the MACS model (and not to the PE distance). We can think
about including a correct PE estimate, but I guess you can properly
deal with PE data just feeding macs with half of the average PE
distance in the shiftsize, i.e. using the options:
--nomodel, --shiftsize=PE/2
You should already have the PE distance estimate from your aligner."

I didn't know the PE distance and he told me that the information was on screen when doing BWA. I repeat BWA step and get the on-screen output. But because BWA processed 256k read pairs in a batch, there was so many information. I still couldn't find what the PE exactly is! Please help me, thanks very very much.
Is the PE the average of "inferred external isize"?


The BWA stderr:
bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (350, 367, 383)
[infer_isize] low and high boundaries: 284 and 449 for estimating avg and std
[infer_isize] inferred external isize from 11191 pairs: 371.316 +/- 20.340
[infer_isize] skewness: -0.213; kurtosis: 0.617; ap_prior: 3.49e-05
[infer_isize] inferred maximum insert size: 507 (6.67 sigma)
[bwa_sai2sam_pe_core] time elapses: 1.93 sec
[bwa_sai2sam_pe_core] changing coordinates of 1273 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 1823 out of 3250 Q17 singletons are mated.
[bwa_paired_sw] 40 out of 354 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.79 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.21 sec
[bwa_sai2sam_pe_core] print alignments... 1.67 sec
[bwa_sai2sam_pe_core] 262144 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (349, 366, 383)
[infer_isize] low and high boundaries: 281 and 451 for estimating avg and std
[infer_isize] inferred external isize from 10673 pairs: 370.950 +/- 20.597
[infer_isize] skewness: -0.258; kurtosis: 0.748; ap_prior: 2.58e-05
[infer_isize] inferred maximum insert size: 508 (6.67 sigma)
[bwa_sai2sam_pe_core] time elapses: 1.78 sec
[bwa_sai2sam_pe_core] changing coordinates of 1206 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 1989 out of 3409 Q17 singletons are mated.
[bwa_paired_sw] 45 out of 297 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.83 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.20 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 524288 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (351, 367, 383)
[infer_isize] low and high boundaries: 287 and 447 for estimating avg and std
[infer_isize] inferred external isize from 10731 pairs: 371.640 +/- 20.047
[infer_isize] skewness: -0.169; kurtosis: 0.458; ap_prior: 2.90e-05
[infer_isize] inferred maximum insert size: 505 (6.67 sigma)
[bwa_sai2sam_pe_core] time elapses: 1.79 sec
[bwa_sai2sam_pe_core] changing coordinates of 1230 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 1980 out of 3295 Q17 singletons are mated.
[bwa_paired_sw] 40 out of 323 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.80 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.22 sec
[bwa_sai2sam_pe_core] print alignments... 1.47 sec
[bwa_sai2sam_pe_core] 786432 sequences have been processed.

[drio]

It is here:

..
[infer_isize] (25, 50, 75) percentile: (351, 367, 383)
[infer_isize] low and high boundaries: 287 and 447 for estimating avg and std
[infer_isize] inferred external isize from 10731 pairs: 371.640 +/- 20.047
[infer_isize] skewness: -0.169; kurtosis: 0.458; ap_prior: 2.90e-05
[infer_isize] inferred maximum insert size: 505 (6.67 sigma)
..

If you prefer, you can redirect the output of your processes to a file and
grab whatever info you need.

[crotoc]

Thanks very much. As you said, should I approximately use 185 (371.64/2) as parameter of --shiftsize, because the inferred external isize is 371,64 in average?

It is here:

..
[infer_isize] (25, 50, 75) percentile: (351, 367, 383)
[infer_isize] low and high boundaries: 287 and 447 for estimating avg and std
[infer_isize] inferred external isize from 10731 pairs: 371.640 +/- 20.047
[infer_isize] skewness: -0.169; kurtosis: 0.458; ap_prior: 2.90e-05
[infer_isize] inferred maximum insert size: 505 (6.67 sigma)
..

If you prefer, you can redirect the output of your processes to a file and
grab whatever info you need.