chromap

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core dumped with some samples

4

Hi, Thanks for the great software. I've been running chromap (`-preset atac -t 8`, otherwise default params) on a lot of samples from the literature, but I'm getting 'core dumped'...

plger

why doesn't chromap require a restriction enzyme option like HiC-Pro?

2

Hello @haowenz: 1. I am wondering how `chromap` handel Hi-C without knowing the information of restriction enzyme? 2. I am testing `chromap` with a Hi-C library using combination of two...

Linhua-Sun

Non barcoded chipSeq data error

5

I am trying to map chipseq data, without providing a barcode file. chromap fails after mapping with the following error: ``` Numbers of reads and barcodes don't match! ``` Does...

xiamaz

scATAC bed file add score and strand

3

Hi~ Thanks for the useful software! Are you considering adding score and Beto the bed file output from single cell ATAC mode? Best, Yumo Song

sonyumo

SAM output broken

10

Hi all, I understand SAM output is not optimized and it is discouraged, however I had to test it and I run into some issues. First of all, output is...

dawe

bam file displays error on IGV

2

``` ❯ chromap --version 0.1-r208 ❯ which igv.sh ~/IGV_Linux_2.8.12/igv.sh ``` When loading the chromap-mapped（0.1-r208） paried-ended bam file to IGV ( version :Linux 2.8.12 ), the forward reads display fine, but...

AssumeAssume

how to extract unique mapped reads?

9

Hi, We have mapped our illumina short reads to our genome using typical commands with --SAM of chromap.  But I failed to find the tag like "NH:i:" or "XT:A:U"...

bilibilij

Forcing chromap to output ALL result

2

Hi, is there any way to force chromap to output all the unmapped and multi-mapped reads? And how are they identified? It was mentioned in issue 20 that multi-mapped reads...

Solyris83

Illegal instruction (core dumped)

5

Ciao ! On a fresh MAESTRO — release 1.5.1 — installation (Ubuntu 18.04 with Python v3.8.12 installed) I tried to run chromap, chromap --version or chromap -h having immediately Illegal...

kOoLiNuS

low map rate for 10X scATAC-seq

24

I'm aligning 10x genomics scATAC-seq to the rheMac10 genome. The sequencing is 50bp for R1 and R2 paired-end sequencing on the Novaseq. The genome was built with k`17` and w`7`...

badoi