Questions tagged [pacbio]
Pacific Biosciences is a biotech company selling a third-generation sequencing technology often denoted by the same name, also known as Single-Molecule Real-Time (SMRT) sequencing. Questions related to data generated by PacBio/SMRT sequencing.
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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 ...
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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 ...
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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,...
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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,...
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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.
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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 ...
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Hybrid assembly versus polishing for hifi and illumina reads
I will have to carry out a project of assembly using hifi reads for which I have already illumina reads and I am wondering which of the hybrid assembly or polishing would be the best option for this ...
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ipdSummary command stops working if --identify m5C_TET is included in command, and does not give any m5C info either
I have installed the latest SMRT Tools (ipdSummary version 3.0). My goal is to extract ipdRatio and modified bases. In the ipdSummary --help command :
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How critical is the "Non-unique read group integer IDs found" warning in running ipdSummary?
I am trying to get the ipdRatio and modified bases information from a PacBio bam file which is sorted and indexed. The command I'm running is:
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pacbio demultiplexing issue
I was wondering if there is a way to provide pacbio lima demultiplexing only a barcode, and let lima demux sample even if only one end has the barcode, not both?
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Finding mutations in glycosylation sites
We are going to look at the likely N- and O- glycosylation sites within MUC16 (Q8WXI7 · MUC16_HUMAN)§ by in house long-read DNA sequencing data (PacBio).
Counting the number of tandem repeats is a ...
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Pacbio HIFI pbmm2 alignment metrics
I am new to pacbio sequencing data. I just did some alignment of pacbio HiFI data using pbmm2. I have the bam now, I would like to collect some metrics on the alignment. I used to work on the illumina ...
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StringTie discovers less novel isoforms when reference annotation is provided
I am analyzing PacBio IsoSeq data and I am using StringTie to assemble transcripts. I noticed the difference in the output files when I add a reference genome annotation (-G option in StringTie). In ...
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regex: samtools command to "refine" PacBio IsoSeq data?
I am working with preprocessed data (IsoSeq PacBio) and I cannot understand one of the steps:
samtools view -b -e [rq] >= 0.9 flnc.bam
What exactly was ...
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How to subset an SRA file for a single chromosome?
I used prefetch to get the Pacbio reads of chicken from the SRA database. I want to align these reads against a reference genome, but not all the reads. I am only interested in a particular region on ...
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