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Duplicated rows in the TAD boundary file given by fac boundaries #163
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Hi, thanks for reporting this! It looks like a bug. |
Hey, can you quickly confirm that it is this file you have been using? https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3262960 |
Okay, I think I have a fix. This seems to be related to "shallow" insulation signal, I think. But I'm pretty sure I found the piece of code that led to the duplication. can you try the fixed version here? |
fanc-0.9.26 indeed resolved my issue! Thank you very much. |
Hi,
I'm trying to call TAD boundaries using
fanc insulation
followed byfanc boundaries
. The results looks fine but I found that several lines are duplicated in the output TAD boundary BED like this:Details:
I used fan-c 0.9.25 and started with a published hic file downloaded from GSE116862.
I first calculated insulation score under 10-kb resolution, trying different window size.
After visually checking the insulation scores with the contact frequency map, I decided to identify the TAD boundaries using window size as 500 kb.
The boundaries in the BED file fits with the contact frequency heatmap well, but 80 lines are duplicated as I shown on the above.
hESC_D05_Rep1.TAD_boundaries.bed.zip
By the way, I also checked the corresponding 500 kb insulation score file and all the rows in this file are unique.
I'm wondering how this happened. Did I use the fan-C in a correct way?
thanks,
Ziyin
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