tabix error to generate WashU browser compatible file

[Hiroyuki Kato]

Hi, 

I'm doing the tutorial presented in 2020 Nature Protocol, and encountered that when performing 

tabix -f -p bed washu_browser_format.bed.gz

The error message says,

[E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used?

The offending line was: "track type=interact name="Your_Fit-Hi-C_Interactions" description="Fit-Hi-C_Interactions" interactDirectional=true useScore=on maxHeightPixels=50:100:200 visibility=full"

[E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used?

The offending line was: "chr1 -1 1 1 inf inf EXP 0 chr1 -1 1 SOURCE_NAME . chr2 -1 1 TARGET_NAME +"

[E::hts_idx_push] Unsorted positions on sequence #458497: 1 followed by 0

tbx_index_build failed: washu_browser_format.bed.gz

Any advice is appreciated.

Best regards,

[Sourya Bhattacharyya]

Hi Hiroyuki,
Please check whether the files "washu_browser_format.bed" and even the FitHiC output "*spline_pass1.res*.significances.txt.gz" are correctly created or not. You can paste the first 4-5 lines from each file if you are not sure about their correctness. Then check the steps 14 and 15 (page 19) from the paper. Specifically, check whether the step 14 has been correctly executed or not.

[Hiroyuki Kato]

Hi Sourya,

Thanks for your reply!

Seems that "washu_browser_format.bed.gz" was not prepared correctly.

Now it works perfectly fine!

Thanks for this wonderful tool!

Best regards,

2021年2月18日(木) 14:56 Sourya Bhattacharyya <sourya...@gmail.com>:

--
You received this message because you are subscribed to a topic in the Google Groups "Fit-Hi-C" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/fithic/PUnlTM5f6ds/unsubscribe.
To unsubscribe from this group and all its topics, send an email to fithic+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/fithic/5d668553-6c3d-4e5f-82ad-96ed956d2f15n%40googlegroups.com.