Juicer does not produce results (eg. merged_nodups.txt)

Biscuite-wzy commented 1 year ago

Hi, Recently, I have used Juicer to analysis my data. I got some results in the aligned file, as follows, but it did not generate merged_nodups.txt. I do not know how to solve it. Can you help me? Thanks

header inter_30_contact_domains inter_30.hic inter_30.txt inter.hic inter.txt merged1.txt merged30.txt merged_dedup.bam

sa501428 commented 1 year ago

merged_nodups.txt has been replaced by the bam and merged*txt files in juicer2. What information are you needing exactly?

Biscuite-wzy commented 1 year ago

Thanks for your reply. I get it.

787117923 @.***

------------------ 原始邮件 ------------------ 发件人: "aidenlab/juicer" @.>; 发送时间: 2022年9月19日(星期一) 凌晨4:02 @.>; @.**@.>; 主题: Re: [aidenlab/juicer] Juicer does not produce results (eg. merged_nodups.txt) (Issue #291)

merged_nodups.txt has been replaced by the bam and merged*txt files in juicer2. What information are you needing exactly?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

YuzhouGong commented 1 year ago

Hello, I installed juicer by gitting clone https://github.com/theaidenlab/juicer.git (so I guess it's juicer 2, the juicer_tools.2.20.00.jar was used), then I run the juicer.sh with -S early along with other necessary parameters, then I got the results in the aligned fold, which included:

inter_30.txt; inter_30_hists.m; inter.txt; inter_hists.m; merged_dedup.bam; merged30.txt; merged1.txt; header.

There is no file called "merged_nodups.txt", but I'm a rookie in genome assembly, so I could just follow the instruction from the PDF "Genome Assembly Cookbook" in which designated merged_nodups.txt file as the input of the 3D-DNA pipeline. 3d-dna input I‘m wondering if there is an updated version of the "Genome Assmbly Cookbook" using juicer 2, or a thorough documentation of juicer 2 demonstrating how to link its produced results in 3D-DNA pipeline? Thanks in advance! BTW, I can't post my question on https://groups.google.com/g/3d-genomics, so I post it here, please forgive that. Yuzhou

XuanZhang-Black commented 1 year ago

Hello, I installed juicer by gitting clone https://github.com/theaidenlab/juicer.git (so I guess it's juicer 2, the juicer_tools.2.20.00.jar was used), then I run the juicer.sh with -S early along with other necessary parameters, then I got the results in the aligned fold, which included:

inter_30.txt; inter_30_hists.m; inter.txt; inter_hists.m; merged_dedup.bam; merged30.txt; merged1.txt; header.

There is no file called "merged_nodups.txt", but I'm a rookie in genome assembly, so I could just follow the instruction from the PDF "Genome Assembly Cookbook" in which designated merged_nodups.txt file as the input of the 3D-DNA pipeline. I‘m wondering if there is an updated version of the "Genome Assmbly Cookbook" using juicer 2, or a thorough documentation of juicer 2 demonstrating how to link its produced results in 3D-DNA pipeline? Thanks in advance! BTW, I can't post my question on https://groups.google.com/g/3d-genomics, so I post it here, please forgive that. Yuzhou

Hi, Yuzhou! I also met the same problem as you. May I ask if you have solved it?

XuanZhang-Black commented 1 year ago

merged_nodups.txt has been replaced by the bam and merged*txt files in juicer2. What information are you needing exactly?

Which file should I choose to use as the 3d-dna input mnd file?

YuzhouGong commented 1 year ago

Hi XuanZhang,

if you add "--assembly" in your juicer2 command, for example like "/home/User/juicer/juicer.sh -t 32 -g XXX -z /home/User/juicer/restriction_sites/XXX_HindIII.txt -p /home/User/juicer/restriction_sites/XXX.chrom.sizes -d /home/User/juicer/work -D /home/User/juicer -s HindIII --assembly", you should be able to get a merged_nodups.txt file in the results.

XuanZhang-Black commented 1 year ago

OK, thank you very much.

wuyh0328 commented 7 months ago

Hi friends! Have you solved your problem? How was it resolved?

XuanZhang-Black commented 6 months ago

Hi! Just add "--assembly" to the end when you run juicer.sh. Hope that may help you.

Best wishes!

发件人：wuyh @.> 发送日期：2023-12-11 15:58:42 收件人：aidenlab/juicer @.> 抄送人：XuanZhang-Black @.>,Comment @.> 主题：Re: [aidenlab/juicer] Juicer does not produce results (eg. merged_nodups.txt) (Issue #291)

Hi friends! Have you solved your problem? How was it resolved? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

wuyh0328 commented 6 months ago

Hi! Just add "--assembly" to the end when you run juicer.sh. Hope that may help you. Best wishes! 发件人：wuyh @.> 发送日期：2023-12-11 15:58:42 收件人：aidenlab/juicer @.> 抄送人：XuanZhang-Black @.>,Comment @.> 主题：Re: [aidenlab/juicer] Juicer does not produce results (eg. merged_nodups.txt) (Issue #291) Hi friends! Have you solved your problem? How was it resolved? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

Thank you very much, as you said, for solving my problem.

aidenlab / juicer

Juicer does not produce results (eg. merged_nodups.txt) #291