Tang JIWEI

Error! HtsLib-error-truncated tabix record

3

@ArtRand `modkit dmr pair -a Y1_5_1_m6A.bed.gz -a Y1_5_2_m6A.bed.gz -b Y2_5_1_m6A.bed.gz -b Y2_5_2_m6A.bed.gz -o Y5dm.bed --header --ref transcripts.fa --segment Y5single_base_segments.bed --base A -t 30 --log-filepath Y5dm.log --careful`  `mod_kit 0.4.5` `tabix...

Inconsistent m6A counts with --ignore; how to compare m5C differences?

4

 `modkit pileup Y1_5_1.bam Y1_5_1.bed --ref transcripts.fa --log-filepath Y1_5_1.log -t 20 --with-header`  `modkit pileup Y1_5_1.bam Y1_5_1_m6A.bed --ref transcripts.fa --log-filepath Y1_5_1_m6A.log -t 30 --with-header --ignore 17596` https://github.com/nanoporetech/modkit/issues/347 @ArtRand 1.Why is...

--ref <REFERENCE_FASTA> is to select the reference genome or transcriptome

2

@rmp When I want to perform m6A analysis and use `modkit pileup` to identify methylation information, should I specify the reference genome or the reference transcriptome with the `--ref `...

failed to get modbase info for record 6bcfdea5-e9eb-4fc9-a72e-81744a77df80, Skipped: AUX data not found

5

@ArtRand @rmp Hey, I received a file named pass.fq.gz, which the company called using Dorado. I then mapped the reads from the .fq.gz file to the transcriptome, when I run...

More than 1 read_group present - split your pod5

20

@Psy-Fer Hi, when I run this command:`blue-crab p2s 20241127-DRS1499-PAY10858-P02.pass.pod5 -o 20241127-DRS1499-PAY10858-P02.pass.blow5 -t 20` there are errors : 07-Jan-25 17:10:51 - blue-crab - [ERROR]: acquisition_id does not match prev value: 0:...

POD5 nanopolish index

4

@satta Hi, The latest ONT RNA004 original file of my DRS data is POD5. How can I use nanopolish to build an index? please

How to reduce duplicate BUSCOs in a HiFi + Hi-C assembly of a 2.5 Gb genome (6.9% heterozygosity, 90% repeats)

2

@lh3 @chhylp123 @molecules Hi, The genome is 2.5 Gb in size, with a heterozygosity of 6.9% and 90% repetitive sequences (a highly repetitive species). Although both HiFi and Hi-C data...

What to do with ioe files with multiple samples?

3

Hi @EduEyras @leipzig The data I used is ONT DRS data, there are 2 species (cultivar and wild species, uniformly aligned to the cultivar genome) with 2 replicates and a...

ERROR:__main__:Unknown error: (<class 'IndexError'>, IndexError('list index out of range'), <traceback object at 0x2b44d38defc0>)

6

Hi @leipzig @EduEyras Here I'm trying to do it in samples to get the GTF for each sample, but it keeps reporting this error `ERROR:__main__:Unknown error: (, IndexError('list index out...