chromap
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haowenz
Fast alignment and preprocessing of chromatin profiles
Hello, The fragment file returned by `chromap` is very useful for scATAC-seq, but sometimes, we need the peak by cell count matrix (or .mtx) for further analysis. Is there a...
The genome is about 3G and come up with Segmentation fault (core dumped) cmd: chromap --preset hic -x reference/genome.index --SAM -1 fastq/HIC508_raw_R1.fastq.gz -2 fastq/HIC508_raw_R2.fastq.gz -r reference/genome.fa -t 20 -o hic.sam...
Hi! Thanks for updated the --read-format option to accommodate the complex barcode by using multiple bc fields. it worked very well. But when I am trying to process some new...
Hi! I'm having an issue when outputting paired end data in SAM/BAM format, where the TLEN column (column 9) are all 0s. I've tested this and had similar issues in...
Hi, thanks for the tool `chromap`, which looks really promising based on the preprint. I'm having trouble creating genome index for human. I don't have any problem with the test...
Hi, Haowen Chromap is super fast when I use pair format. But I want to use chromap for assembly scaffolding pipeline (chromap + yahs), espeically for large plant genome. Since...
I need to use deeptools to analysis my bulk ATAC-seq data. However, deeptools require a bigwig (.bw) file for most of the analyses. I have tried two pipelines to generate...
Hello. Is there any limit to the length of chromosomes in chromap? I'm working on an contact map for genomes with chromosomes greater than 2GB, and some other alignment tools...
Chromap is indeed an ultrafast tool. Thanks for developing and this method. However, I have encountered two problems when I using chromap with scATAC-seq data. The first one is that...