Wenchao Zhang

vg index command was killed

4

Hi, Sir, I download the graph file **1000GPlons_hs38d1.vg** from https://cgl.gi.ucsc.edu/data/giraffe/mapping/graphs/for-NA19239/1000gplons/hs38d1/. Then, I use "vg index -x 1000GPlons_hs38d1.xg -g 1000GPlons_hs38d1.gcsa -k 16 1000GPlons_hs38d1.vg", then it was killed without any message. But...

I am interesting in the fusion_finder.py and hope to find the true positive fusion transcript, however, I am struggling for a long while to find other evidences to support the...

Hi, Magdoll, I have download the [fusion fasta](http://datasets.pacb.com.s3.amazonaws.com/2015/IsoSeqHumanMCF7Transcriptome/IsoSeq_MCF7_2015edition_polished.fusion.fasta) file and used the same commands and parameters at (https://github.com/Magdoll/cDNA_Cupcake/wiki/Best-practice-for-fusion-transcript-finding) 1) minimap2 against hg38 & sort 2.) fusion_finder.py , 3.) SQANTI (gencode.v33)...

Always report ERROR: path to the matrixfile is not valid.

3

Hi, Dear HiNT developer, Thanks for developing this HiNT. I have successfully installed HiNT. I am using hint tl. But it always return ERROR: path to the matrixfile is not...

OSError: [Errno 5] Input/output error

4

Hi, yfukasawa, I am running LongQC for a batch of my Pacbio unaligned BAMs. For the small samples, it run smoothly. But for one of a little bit large BAM...

Could you recommend some tools/platform to directly generate the SV breakpoints from Hi-C data, and can be used by NeoLoopFinder?

4

Could you recommend some tools/platform to directly generate the SV breakpoints from Hi-C data, and can be used by NeoLoopFinder? I prefer to simple or linux command line format.

Could you give me some guidelines to manually review and validate the neoloops and neotads

1

Xiaotao, I am using neoloop to produce some neo-loops and neo-tads (some rows with the last columns as "1"). But I am interested in validate whether they are really neo-loops/...

Some questions for positive and negative training dataset

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Xiaotao, 1.) In your NC peakachu paper, Fig.1 mentioned GM12878 is used for the training dataset. But in the Supplementary Data 1, GM12878, K562, H1ESC, and mESC are used for...

How to output the Regular loop and Tads without SVs

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Hi, Xiaotao. I am now using NeoloopFinder to detect Neoloops/Neotads. But I found one Neoloop was not reported (even the last column tag as 0) from NeoloopFinder. I traced back...