mnd files

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Sergej Nowoshilow

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Oct 10, 2017, 7:53:58 AM10/10/17
to 3D Genomics
Dear all

Is there a way to create the mnd files manually? I have created BAM files using Bowtie2 and am looking for a way to convert them to mnd somehow, because I don't really want to re-run the mapping as it takes several days for my data.
I looked into the mnd file and it looks simple, however, I cannot quite figure out the format. Do you have an idea where I can lookup the description of the format? Then I'd simply run 3D DNA using my own manually created mnd files.

Thanks a lot!
Sergej

Muhammad Saad Shamim

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Oct 10, 2017, 8:17:40 AM10/10/17
to Sergej Nowoshilow, 3D Genomics
Hi Sergej!

It certainly is possible to convert files to the mnd format and then create a hic file.
Descriptions of the different mnd formats are available here: https://github.com/theaidenlab/juicer/wiki/Pre#file-format 

​Best,​

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Neva Durand

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Oct 10, 2017, 8:29:54 AM10/10/17
to Muhammad Saad Shamim, Sergej Nowoshilow, 3D Genomics
Hi Sergei,

One possibility is to convert it to sam and run chimeric_blacklist.awk on the sam. The sort.txt result should then be run with fragment.pl to get the fragment numbers and the resulting file sorted (see the juicer script for exact sort command). Then you can run juicer in the “dedup” stage. 

Note that bowtie is not recommended as it doesn’t handle chimeric reads well; you will lose a lot of reads that are actually ligation products. 

Best
Neva



On Tue, Oct 10, 2017 at 8:17 AM Muhammad Saad Shamim <sa50...@gmail.com> wrote:
Hi Sergej!

It certainly is possible to convert files to the mnd format and then create a hic file.
Descriptions of the different mnd formats are available here: https://github.com/theaidenlab/juicer/wiki/Pre#file-format 

​Best,​
On Tue, Oct 10, 2017 at 6:53 AM, Sergej Nowoshilow <sergej.n...@gmail.com> wrote:
Dear all

Is there a way to create the mnd files manually? I have created BAM files using Bowtie2 and am looking for a way to convert them to mnd somehow, because I don't really want to re-run the mapping as it takes several days for my data.
I looked into the mnd file and it looks simple, however, I cannot quite figure out the format. Do you have an idea where I can lookup the description of the format? Then I'd simply run 3D DNA using my own manually created mnd files.

Thanks a lot!
Sergej

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Sergej Nowoshilow

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Oct 10, 2017, 8:58:13 AM10/10/17
to 3D Genomics
Hi Muhammad,

yeah, I saw that link, however, I wasn't quite sure. Because if I open the MNT file which you can download from the NCBI, you suddenly see that the first column is either 0 or 16. In the description you see that it's either 0 or *anything else*, but it wasn't quite obvious why they use 16 and not 1, for instance. 
But thanks! I will read in more detail!

Best
Sergej


Am Dienstag, 10. Oktober 2017 14:17:40 UTC+2 schrieb Muhammad Shamim:
Hi Sergej!

It certainly is possible to convert files to the mnd format and then create a hic file.
Descriptions of the different mnd formats are available here: https://github.com/theaidenlab/juicer/wiki/Pre#file-format 

​Best,​

On Tue, Oct 10, 2017 at 6:53 AM, Sergej Nowoshilow <sergej.n...@gmail.com> wrote:
Dear all

Is there a way to create the mnd files manually? I have created BAM files using Bowtie2 and am looking for a way to convert them to mnd somehow, because I don't really want to re-run the mapping as it takes several days for my data.
I looked into the mnd file and it looks simple, however, I cannot quite figure out the format. Do you have an idea where I can lookup the description of the format? Then I'd simply run 3D DNA using my own manually created mnd files.

Thanks a lot!
Sergej

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Sergej Nowoshilow

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Oct 10, 2017, 9:01:46 AM10/10/17
to 3D Genomics
Hi Neva

thanks a lot! I'll give it a try.


> Note that bowtie is not recommended as it doesn’t handle chimeric reads well; you will lose a lot of reads that are actually ligation products. 
So, what I actually do is to run the reads through the HiCUP pipeline that should remove all invalid pairs of reads. If I then look at the alignments of the remaining reads in the genome browser they all look fine. 
Do you think I can process the HiCUP-BAM file the way you described? Or is it better to start from scratch using BWA?
The problem is that BWA (or actually, juicer in general) takes ages and I'd like to give 3D DNA a try as soon as possible just to have an impression whether it can be used to tackle my problem.

Thank you!
Best
Sergej

Neva Durand

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Oct 10, 2017, 9:34:17 AM10/10/17
to 3D Genomics, Sergej Nowoshilow
Hello Sergej,

BWA shouldn’t take forever (nor should Juicer). What system are you running on?  You can adjust the number of threads used by BWA to run faster. 

As for the question about “16”, this is just the flag from BWA for reverse strand. Strand only matters for deduping. 

Are your reads already deduped?  Do they have a fragment number assigned?

Best 
Neva


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Sergej Nowoshilow

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Oct 12, 2017, 4:36:28 PM10/12/17
to 3D Genomics
Hi Neva

Sorry for the delay. I got it to run! Thanks a lot for the advice.

Best
Sergej
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