Continue the pipeline from BAM mapped by BWA

[svm-zhang]

Hello @nservant,

Thanks for HiC-Pro! I am new to HiC-Pro.

My question is: if I have aligned my R1 and R2 reads using BWA, respectively, what should I do to incorporate them into the pipeline? I know how to get the unmapped reads from global mapping, but not sure what to do to trim these unmapped reads.

Any help would be appreciated.

Happy new year!

Simo

[taylorreiter]

+1

[lucaspatel]

Also +1. Would really appreciate some support on this issue.

[ChenFengling]

+1. My Hi-C data is BL-Hi-C data which doesn't need the local mapping step. Meanwhile, why I have to use BWA is that the Bowtie takes 17 hours with default setting on my sample while BWA needs only 5 hours. Bowtie setting: BOWTIE2_GLOBAL_OPTIONS = --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder BWA command: bwa mem

So, should I change the settings or just use .bam file from BWA results.

If I simply put the BWA mapped bam in bwt2, I got the error like: make: *** [bowtie_pairing] Error 1 .

[nservant]

Thanks for your feedback. Just two questions ;

• What is BL-Hi-C :) ?
• And which type of BAM do you have, is it paired BAM file ? or do you still align R1/R2 independantly ? Thanks

[kainblue]

Hi All,

Anyone got a conclusion yet? Can we use the bam from BWA to fit into HiC-Pro?

Thanks

[nservant]

Hi, Not yet. This is still in my top priority, but I did not have time to look at it so far. Sorry. N

[magnitov]

Hi @nservant,

Have you updated the HiC-Pro to use bwa mapped BAM files? Couldn't really find the info, so just curious.

Best, Mikhail