chromap
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haowenz
Fast alignment and preprocessing of chromatin profiles
Thanks for your great work in developing Chromap, an ultrafast aligner for chromatin profile alignment! In the paper, you mentioned that Chromap is much faster than popular aligners such as...
the language in the manpage for -1 is a little confusing: "read11.fq,read12.fq,read13.fq" Can you consider changing it to something more explicit that will reflect how most people with use the...
Hello, First of all, thank you for developing chromap. It saves me tons of mapping time :) For a feature request, I am wondering if the chromap could generate sth...
Hi, We have a ATAC/RNA-seq pair-end reads for the input. What kind of options should we be using for the mapping part? What should we expect for the output?
Hello, I want to run chromap using my genome file But, coredumped went out Here is the log file and command Command $chromap -i -r Combined_pseudohap.phased.filtered.0.arcs.fasta -o chromap.index -t 100...
The summary file generated is as follows, I'm so confused as, why the unmaped is minus zero.(the barconde is empty) > barcode,total,duplicate,unmapped,lowmapq > ,66319792,2753815,-54606110,12185252 > and the following is the...
Dear you, Thanks for the continued updates, the high speed of chromap is really helpful for giant genomes like wheat! I'm dealing with Wheat Hic data, because of the similarity...
# Problem Different ValidPairs rate between chromap and bowtie2 in HiC data using [HiC-Pro](https://github.com/nservant/HiC-Pro) pipeline, which convert bam into *.VailidPairs format and stat. When I use chromap, result is: Dumped_pairs_rate%:...
Hi I am using the software chromap developed by you for map HiC reads, but an error occurred during the alignment. I hope to get your help. The following is...
Hello Chromap Team, Thank you very much for actively maintaining the chromap! I recently used Chromap for mapping scATAC-seq data with a barcode whitelist. I found that the log file...