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novoalab / EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
GNU General Public License v2.0
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sam file creation stuck #63

Closed aman21392 closed 3 years ago

aman21392 commented 3 years ago

I used this command as you mentioned in the variants.py script but ---- minimap2 --MD -t 70 -k 5 -ax map-ont /Drive4/Homo_cdna.fa /Drive8/combined_T.fastq >E6.sam

It running from 2 days and there is no increase in the size of the file - [M::mm_idx_gen::7.2891.39] collected minimizers [M::mm_idx_gen::7.6882.92] sorted minimizers [M::main::7.7212.91] loaded/built the index for 250156 target sequence(s) [M::mm_mapopt_update::7.7212.91] mid_occ = 1510760 [M::mm_idx_stat] kmer size: 5; skip: 10; is_hpc: 0; #seq: 250156 [M::mm_idx_stat::7.722*2.91] distinct minimizers: 396 (0.25% are singletons); average occurrences: 184315.192; average spacing: 5.407; total length: 394654324

It stuck here from 2days can you please suggest me what is the problem. Thanks in advance

aman21392 commented 3 years ago

I just want to know is there any logic to used --MD and -k 5 OR i can directly used default settings of minimap2 to create sam file. Thanks in advance

aman21392 commented 3 years ago

I just run these command and these will give bam file now. So is it fine. Thanks minimap2 -ax map-ont -t 70 Homo_cdna.fa /Drive4/combined_T.fastq | samtools view -@40 -hSb - | samtools sort -@ 40 -o E6.bam

Huanle commented 3 years ago

Hi @aman21392 ,

I am glad to know you made minimap2 work. --MD tag allows inferring indels without looking at reference sequences. -k, the minimizer, will change mapping sensitivity. Trying different minimizers, you will have different amount of reads mapped.

Best,

weir12 commented 3 years ago

Hi @aman21392 I had met the same problem as you, and then I solved it by increasingk to 14 and selecting splice mode