ming1211

@loraince @haowenz Dear Loraince. I'm doing similar work as yours but I can't generate bigwig file successfully. Can you please share the commands you used after getting the bed file...

I see! Thanks for your reply! It's very helpful, I will try -q 0 and update with you! Thanks again! Li Song ***@***.***> 于2023年10月6日周五 18:01写道： > Chromap internally automatically conducts...

Thanks for your update！I tried, it's perfect now! And I got another question, when preset as ATAC, there are 2 parameters inside: --remove-pcr-duplicates --remove-pcr-duplicates-at-cell-level, So if deal with bulk-ATAC seq,...

not single-cell.

Thanks for your promt reply！！ 0.2.3-r407 this is the version got after the command chromap --version I retried just now, using fastq data trimmed by fastp. then the Error below...

Thank you again. I'm using the newest version of chromap. but the bed output didn't even generate. the Error is as follows. chromap: src/temp_mapping.h:42: void chromap::TempMappingFileHandle::InitializeTempMappingLoading(uint32_t) [with MappingRecord = chromap::PairedEndMapping...

`chromap --preset chip -x /genome/tair_10/chromap-tair10_all -r /genome/tair_10/lower_TAIR10_Chr.all.fasta -1 CRR303826_f1-paired.fq.gz -2 CRR303826_r2-paired.fq.gz -o CRR303826_chromap.bed` It is the command I used. I'm sure that I have the permission.

Hi, Dear Mourisl, Thanks for all your reply. I retried Chromap several times. But the results are still always unsatisfactory. the chromap version is 0.2.3-r452 ``` cmd="$pathTochromap -i -r /SollycM82_v1.0.fasta...

> Build index for the reference. > Kmer length: 17, window size: 7 > Reference file: /SollycM82_v1.0.fasta > Output file: ./chromap-M82_all > Loaded all sequences successfully in 7.81s, number of...

this is a single-end data.