Juicer as input for SALSA

Dustin Sokolowski

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Apr 6, 2021, 12:29:32 PM4/6/21

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Hello!

Thank you for your fantastic tool. I am building a trio-binned diploid genome and I was hoping to correct for mis-joined scaffolds using both 3d-DNA and the SALSA2 pipelines so I can compare afterwards.

This being said, I was hoping to pre-process my Hi-C data with juicer regardless of if I follow it with 3d-DNA or SALSA2. Salsa2 requires a bed file of aligned, deduplicated reads ( bamToBed -i deduplicated_HiC.bam > deduplicated.bed) but I'm not sure how to get the appropriate file for SALSA. I was thinking that it could maybe be made from the merged_nodups.txt file but I don't want to cause any errors. Any advice on this would be fantastic.

Thanks so much!

Dustin

Olga Dudchenko

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Apr 6, 2021, 3:15:55 PM4/6/21

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Hello Dustin,

I believe Neva already responded to this. You can also create a bam file from the alignments found in the splits folder (though you'll need to dedup them separately and the contacts won't be identical).

Olga

C T

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Aug 24, 2021, 9:54:37 AM8/24/21

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Hi,

I have the exact question on using output from juicer for input to SALSA2. Can you please elaborate? As OP, I was also thinking about using merged_nodups.txt as input.
Thank you,

Cenny

C T

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Aug 24, 2021, 10:13:32 AM8/24/21

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Sorry. To be more specific, does juicer output deduplicated bam files? If not any suggestion on the easiest way to get the deduplicated bam files from juicer output files.

Thank you!

CT

Dustin Sokolowski

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Aug 26, 2021, 1:23:33 PM8/26/21

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Hey CT!

Juicer-2.0 offers deduplicated sam files which can easily be converted to Bam format. I ended up using this. It is in more of a beta but I used the CPU version and asked for 100 hours across 50 threads and could align and deduplicate an input of 1 billion reads or so. This output is compatible with salsa. While the CPU version works nicely, the PBS version still has some kinks and I can't speak on the other versions, Neva likely can. Hope this helps and am happy to answer any other questions (though as just a user rather than developer I may not be so helpful).

Best,

Dustin

juicer v2: https://github.com/aidenlab/juicer/tree/encode/CPU

C T

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Sep 1, 2021, 3:00:39 PM9/1/21

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Hi Dustin,

Thanks for your email. Appreciate it!

I'm currently in the middle of running juicer-2.0, the SLURM version. I'll probably switch to CPU version if it doesn't work.

Thanks!

Cenny

Dustin Sokolowski

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Sep 1, 2021, 7:20:24 PM9/1/21

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Awesome, good luck!

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C T

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Sep 7, 2021, 1:23:51 PM9/7/21

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Hi Dustin and anyone else who can help,

I was running juicer.sh from SLURM folder in the encode version.

I ran into an error because juicer.sh tries to run juicer_tools statistics but this command is unknown.

This is the exact error:

/opt/scripts/common/juicer_tools statistics restriction_sites/A673_HiFi_hifiasm_asm_bionano_hap1_Arima.txt outputdir/inter_30.txt outputdir/merged30.txt A673_HiFi_hifiasm_asm_bionano_hap1

WARN [2021-09-07T17:03:59,187] [Globals.java:138] [main] Development mode is enabled

Exception in thread "main" java.lang.RuntimeException: Unknown command: statistics

at juicebox.tools.HiCTools.main(HiCTools.java:96)

This is the version I'm running:

/opt/scripts/common/juicer_tools -V

WARN [2021-09-07T17:19:50,855] [Globals.java:138] [main] Development mode is enabled

Juicer Tools Version 1.22.01

I appreciate it if someone can help me figure out what I should do.

Thanks!

Neva Durand

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Sep 7, 2021, 1:36:32 PM9/7/21

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You need a newer version of the juicer_tools jar.

Best

Neva

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Assistant Professor | Molecular and Human Genetics

Aiden Lab | Baylor College of Medicine

www.aidenlab.org

C T

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Sep 7, 2021, 4:37:40 PM9/7/21

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I thought juicer tools v 1.22.01 is the newest version? I downloaded it from https://github.com/aidenlab/juicer/wiki/Download

Where can I find the newer version?

Thank you!

C T

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Sep 13, 2021, 9:42:52 AM9/13/21

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Hello,

Can someone please let me know where I can find the newer version of juicer tools?

Also, is merged_dedup.sam in the aligned folder the deduplicated sam file?

Thank you!

Dustin Sokolowski

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Sep 13, 2021, 9:49:18 AM9/13/21

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Hey!

The newer version of juicer is in the ENCODE tree: https://github.com/aidenlab/juicer/tree/encode/CPU

the merged_dedup.sam sam file should be the final file indeed! If the version you're running has that file instead of the merged_dedups.txt then I think you're good (though I'm just a user as well)

Also I haven't come across your specific error before but it looks like the version of java that your juicer calls uses an older version of java that is missing some functions juicer needs?

Juicer has this line `java -version 2>&1 | awk 'NR==1{printf("%s; ", $0);}' >> $headfile` which is possibly pulling a version of java that is incompatible? Neva would know much better though.

Best,

Dustin

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C T

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Sep 13, 2021, 10:58:05 AM9/13/21

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Hi Dustin,

Thanks for your email. I am going to try the merged_dedup.sam file then. Appreciate it.

I am hoping the authors/developers or Neva can help me with this.

I cannot find the newer version of juicer_tools.jar in the ENCODE tree. juicer_tools v1.22.01 is the newest version I can find.

In case this helps, this is the java version I'm using:

java -version

openjdk version "1.8.0_151"

OpenJDK Runtime Environment (build 1.8.0_151-8u151-b12-0ubuntu0.16.04.2-b12)

OpenJDK 64-Bit Server VM (build 25.151-b12, mixed mode)

Thanks,

Cenny

C T

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Sep 14, 2021, 10:54:52 AM9/14/21

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Hello,

Can someone please help me find the newer version of juicer_tools? I feel like I'm really close to successfully running juicer encode version to completion. I only need the newer version so juicer_tools statistics does not generate an error.

Thank you!

Ct