Malini Nemalikanti

Hello! Is it possible to use the HiCPro output files (.allvalidPairs or matrix files) as an input for GOTHiC tool (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0174744#sec001) I want to extract significant interactions using GOTHiC and...

Ligation site in configuration file

4

Hello! I wanted to know how the ligation site is to be given in the configuration file. I suppose for HindIII since the cut site is A^AGCTT the reverse complement...

Hello, Since the HipSTR does not have a multi-threading support, to ease the compute time I have processed the data by dividing the regions of the BED file into 100...

HipSTR not taking the motif lengths > 9

1

Hello, I have been trying to use HipSTR on the repeat loci, with motif lengths upto 15bp. I get an error for the regions with motif lengths greater than 9bp....

Hello! I get this error while running Squid. The chimeric sam file generated through STAR run is empty and it fails when run as a bam file with Squid. Please...

Hello! I was wondering if there is an option for the number of threads that can be used by Squid

Hi! I have been trying vcfToBedpe on my MANTA outputs. I also need strand information to be used with ShatterSeek downstream. But both STRAND_A and STRAND_B have ".". Would be...