Questions tagged [long-reads]
Questions relating to long reads, such as pacbio or nanopore reads.
53
questions
1
vote
0
answers
11
views
macs3 to detect high coverage regions in long-reads
I am using macs3 to detect regions with high number of reads, similar to macs3's goal - detect chip-seq peaks - as it has been used for long-reads data, I would like to ask how to determine if it is ...
- 169
1
vote
1
answer
36
views
Aligners for repetitive sequences
we are interested in detecting repetitive sequences in two cell lines, however, when performing the alignment with pbmm2 on GRCh38, not good results are obtained. We are trying to modify the ...
- 169
1
vote
0
answers
17
views
Problems with pbmm2 alignment after subsampling
I have tested pbmm2 align on my total set of reads. However, the alignments are poor. Therefore I am trying to optimize the parameters with a few of them. After doing a subsampling with samtools -s 0,...
- 169
1
vote
1
answer
45
views
how to see pacbio reads in IGV
This question has also been asked on Biostars
I recently used pbmm2 to align my reads to the reference genome, when I specified --sort option it is generated a file with extension bam.bai. Afterwards,...
- 169
1
vote
1
answer
59
views
Indexing the reference genome my process is killed
I am trying to use pbmm2 to create a reference genome index.
I'm on a cluster server, I don't know if that's the reason why it has been killed.
...
- 169
0
votes
1
answer
61
views
Novogene sequencing archives
We have recently received the sequencing files from this company. For each sample, two files with extension Bam and bam.pbi are available. I would like to ask what is the meaning of the numbers behind ...
- 169
1
vote
1
answer
31
views
Finding insertion in a plasmid
This question was also asked on Biostars
I received a set of Nanopore long reads of a ~3kbp long known plasmid with an unknown insert between 1kbp and 7kbp. Could you suggest a pipeline to assemble ...
- 121
2
votes
2
answers
68
views
Longstitch error make: command: Command not found *** No rule to make target
I installed Longstitch and ran the test script with no issues. The output files matched the expected output files. But when I am now trying to run Longstitch on my own data I am getting this error.
<...
- 21
2
votes
2
answers
69
views
Calling isoforms from long read data generated from partially degraded RNA
What will be the best tool to call isoforms from long read data generated from partially degraded RNA. By mistake we processed some samples with poor quality RNA to generate long read. Now we are ...
- 191
3
votes
0
answers
32
views
Can multiplexing in Sequel II SMRTcells reduce the coverage?
I would like to have high depth of coverage of the transcriptome, but I need to analyze several tissues. I was suggested to pool all 5 tissue samples in same SMRT 8M cell. Will this result in a ...
- 307
2
votes
1
answer
278
views
somatic SNV tool for ONT samples
I'm looking for a tool to call somatic single nucleotide variations on reads from an Oxford Nanopore Technologies (ONT) run.
I have both tumor and normal samples and have already aligned them to a ...
4
votes
1
answer
89
views
Tree Building Algorithm that treats gaps as deletions
I'm part of a nanopore sequencing experiment that will sequence several generations of viruses. The intent is to perform directed evolution by putting selective pressure on these viruses and tracking ...
- 51
1
vote
1
answer
366
views
What is a PacBio "movie file"?
I came across references to "movie files" from PacBio sequencing in this paper:
https://www.jimmunol.org/content/204/12/3434
Specifically:
Movie files used to generate results presented in ...
- 957
1
vote
1
answer
1k
views
Oxford nanopore promethion; does guppy3 separate fast5 into pass and fail? If not what does?
just a quick question about fast5 pass fail folders. I have been working under the assumption that the fast5 pass fail folders I was given as raw data from our ONT vendor came from them doing base ...
- 579
1
vote
1
answer
2k
views
Upgrading guppy basecaller on Oxford Nanopore Gridion via PPA
I am trying to update the guppy_basecaller (current version installed is 3.2.10+aabd4ec) on a ONT Gridion device. I am initially trying to update it via the ...
- 283