yos-sk / nanoem Goto Github PK

Hi, thank you for the tool. I have been trying to use it but I don't seem to get past mapping.

If I use minimap2/2.22 it goes incredibly slowly for a 24Gb fastq that should be mapped relatively faster, and haven't manage to make it finish before being killed. And with version 2.17-r941 that is the main one I use I keep having the same error:

[M::main::8.8520.60] loaded/built the index for 34 target sequence(s)
[M::mm_mapopt_update::9.0070.61] mid_occ = 21211
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 34
[M::mm_idx_stat::9.115*0.62] distinct minimizers: 7329827 (9.49% are singletons); average occurrences: 107.956; average spacing: 5.271
[main_samview] fail to read the header from "-".
samtools sort: failed to read header from "-"

I've explored my fastq files and the genome and they seem normal, not sure what might be happening. Any idea what might be going wrong?

Thanks,
Cora

Hi, thanks for sharing this useful tool.

Can I ask which tool do you use to trim adapter for nanoEM dataset before mapping to the reference genome?

Hi,
thank you for the very useful tool!

I have to questions:

In step 4 it says: python src/best_align.py --bam1 1.sorted.bam --bam2 2.sorted.bam --fastq fastq
by --fastq fastq, do you mean the original readout from nanopore, previously called "1d_pass.fq.gz" or something else?

In step 5 $ sambamba mpileup output_CT.sorted.bam -L cpg_sites.bed -o pileup_CT.tsv -t 6 --samtools -f hg19.fa

I always get the error: sambamba-pileup: Unexpected 'f' when converting from type string to type long
Has anybody experienced the same error?
The only way I found to solve it was to omit the "-L cpg_sites.bed" which is no final working solution.
Which cpg_sites.bed file did you use?

I appreciate any suggestions,
kind regards