Out of 70041 loci 70041 were discarded with biases not in range [0.5 2] about fithic HOT 3 OPEN

On Fri, Jul 15, 2022 at 17:06 Nisar Ahmed ***@***.***> wrote: Hi, Thank you for such a nice tool for Hi-C data processing! I am processing DNase-HiC data. I want to apply Fithic2 to my data; I have prepared the input files from HiC-Pro. For example: -i [image: Screen Shot 2022-07-15 at 4 25 27 PM] <https://user-images.githubusercontent.com/108051500/179232277-494d7dca-85d4-4459-aeb3-47468ae2c584.png> -f [image: Screen Shot 2022-07-15 at 4 27 43 PM] <https://user-images.githubusercontent.com/108051500/179232574-147cdb8c-e4b8-419b-8fad-f93fe1ba78a2.png> -t [image: Screen Shot 2022-07-15 at 4 28 24 PM] <https://user-images.githubusercontent.com/108051500/179232686-89933281-a487-421d-8d03-e4f31eb1fe74.png> I proceed to fithic with these input files; however, I encounter error #42 <#42>. After, reading all comments about #42 <#42> and #39 <#39>, I have removed the biases using: awk '{if ($3 > "0.5" && $3 < "2"){ print}}' and from fragments file I've removed all the validpairs with 0 using: awk '{if ($4 > "0" && $5 > "0"){print }}'. After, that now I have -t [image: Screen Shot 2022-07-15 at 4 38 14 PM] <https://user-images.githubusercontent.com/108051500/179234416-bc89e5dc-793a-4455-bd5f-50cbfbc3f49e.png> -f [image: Screen Shot 2022-07-15 at 4 37 20 PM] <https://user-images.githubusercontent.com/108051500/179234276-13236400-031b-4847-a342-b869afdfac5a.png> After this trimming these files, I used this command to run Fithic: - fithic -i fithic.interactionCounts.gz -f fragmentMappability.gz -t biases.gz -r 10000 -o ./fithic-out3/ After Fithic2 ran successfully on my files, when I checked the log file, I noticed that " *Out of 70041 loci 70041 were discarded with biases not in range [0.5 2]*". Here, is the log file: [image: Screen Shot 2022-07-15 at 4 54 35 PM] <https://user-images.githubusercontent.com/108051500/179237471-5fccf3db-9021-4dc2-826b-5afc16daad5c.png> And my significance file has all the values are equal to zero and this is the significance file: [image: Screen Shot 2022-07-15 at 4 56 39 PM] <https://user-images.githubusercontent.com/108051500/179237831-d4227e95-44c3-43b3-89a1-5e48c07f2bf9.png> I am wondering how to resolve this issue. I don't know where I am making mistakes. I really appreciate it if you have a look into this and help me to fix this problem. Thank you! Best, Nisar — Reply to this email directly, view it on GitHub <#56>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEJTNJBB37JDDVQRQ3OIDMDVUFV6NANCNFSM53VWU54A> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>