chromap

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ATAC-seq single end?

3

Hi, I understand that the default mapping option for the ATAC-seq data is pair ended, but is there a mapping option for a single ended ATAC-seq data? Thank you, Lindsay

lindsayhrlee

[BUG] Manpage is down

1

The link to the documentation is broken.

emattei

multi-mapped reads

3

Hi, For the Hi-C data mapping, is there a way to output multi-mapped reads (bolded in the log below) separately? Or is there a way to extract _only_ multi-mapped reads...

lindsayhrlee

[BUG] output to /dev/stdout

4

**Describe the bug** When I use /dev/stdout instead of the output of the -o argument, the program reports an error, saying "Assertion 'temp_mapping_output_file! = __null' failed. "So I can't use...

lvyunyunSCI

Failure to load cellular barcodes containing Ns

3

Hi everybody, Running chromap in the scATAC modality with the command: ``` chromap -q 0 -t 8 --min-read-length 20 --preset atac --SAM -x ${index_file} \ -r ${fasta_file} -1 $r1 -2...

ste-depo

why so slow?

2

Hi Haowen, I used the following command for chromap mapping: ` chromap --preset hic -x $index -t $cpu -q $mapQ -r $asm -1 $read1 -2 $read2 --SAM -o $asm.hic.aligned.Q_"$mapQ".sam `...

zhaotao1987