ming1211

[BUG] summary and log are confusing.

6

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...

how to keep multi-mapped paires for HiC data.

1

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...

Chromap miss some region when deal with Hetero Chromatin

3

Thanks for Chromap wihch is really really helpful especially when dealing with very big dataset. But I found that Chromap miss some region when deal with Hetero Chromatin As shown...

compared with Bowtie2.

3

Thanks for your great software, which is much more time-saving! we used to use bowtie2. Comparing with it, the results are different between these 2 softwares. Much appreciated if you...

incomplete bed output file generated from Chromap with Chip-seq data

19

I tried twice, one used raw_data `chromap --preset chip -t 24 -x chromap-tair10_all -r lower_TAIR10_Chr.all.fasta -1 CRR303826_f1.fq.gz -2 CRR303826_r2.fq.gz --trim-adapters -o CRR303826_chromap.bed ` but the bed output contains incomplete lines...