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convert supplementary reads to primary in sam or bam

I have a problem with a tool, that possibly ignores supplementary reads. I want to find out a bit how this tool works by converting all supplementary reads to primary reads, and then change the names of those reads (because I guess that primary…
Fini
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How to normalise scRNASeq data for differential expression analysis

I wish to perform differential expression analysis for cluster-specific gene expression in single-cell data (with a tool such as MAST or SCDE). I have data for 3 biological replicates. I performed analysis on 10x data with cellranger and have…
Tom Kelly
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Does Prokka do six-frame translations?

Does Prokka do six-frame genome annotations? The corresponding publication does not mention it. Seemann, Torsten. 2014. “Prokka: Rapid Prokaryotic Genome Annotation.” Bioinformatics 30 (14): 2068–69.
Soerendip
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2 answers

Control width of samtools tview "snapshot" when redirecting

I have a large number of loci I would like to examine manually with samtools tview. Rather than typing or copy-n-pasting dozens of coordinates, I was hoping to automate the generation of pileup "images" (text files). With some experimenting just…
Daniel Standage
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Is there a way to import tables in PubMed Central to MySQL or other Relational databases?

I need to use these PMC tables from the medical journals for the purpose of integrating the data with a decision-making software. Though, I can see that one can access full-text for an article from PMC here (which includes the article table), but is…
PinkBanter
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Database of Cell Volumes by Cell Ontology?

Are there any databases that have aggregated information on cell volumes? Most useful would be a database keyed by cell ontology (e.g., CL:0000236 for B cell). The BioNumbers book has a small table, but none of the references appear to link back to…
merv
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Identifying Indels from Chromatograms

I have around 100 chromatograms (.ab1 files) from Sanger sequencing a genome at loci believed to have an indel. I'm new to interpreting this kind of data in general, but I've read a bit on the general idea—mostly in guides like this. What I'm not…
Randoms
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Rule Extraction from nnet results

I used a script in R language that uses nnet library to predict promoter bacteria and i would like to know how to extract rules from this neural network results. As my input of the neural network i have n positive examples of promoter and n false…
Rafael Coelho
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What are the ways to process a list of differentially expressed genes?

We are studying six different human macrophage/dendritic cell types isolated from healthy skin. They all differ from each other in a few cell surface markers. We are interested in the characteristics of each cell type ("marker" genes or biological…
Peter
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Why is a PacBio read length larger than the aligned reference region?

I recently had some Iso-Seq sequencing done on my organism catfish on the new Sequel platform and got weird alignments for a size selected 4 Kilobase and up fraction after running the isoseq3 pipeline. When I investigated the exon intron junctions…
user1238097
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How to find all variable-length seqs with an exact 5' and 3' match in a FASTA file

Context I am interested in finding all of the promotors specific to a particular sigma factor. I have identified the -35 and -10 sites from the literature, bold denotes -10, -35, binding sites: -35 site -10 site 5'…
syn_bio_delta
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Derive a GTF containing protein coding genes from a GTF file with Exons and CDS

Why I need a compatible file I’m trying to run velocyto with the R package to analyse RNA velocity (cell trajectories) with single cell RNASeq data. I have performed single cell analysis from 10x Genomics data using cellranger. I have successfully…
Tom Kelly
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MrBayes runs as single-core, but hangs when multi-core

I compiled MrBayes v3.2.7 from github, with the configuration options ./configure --without-beagle --enable-mpi. The program is called mb. I tried one of the included example files "sceloporus.nex". I find that if I run mb sceloporus.nex, then it…
Pascal
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Understanding the initialization of the Needleman-Wunsch algorithm

I would like to ask why when we initialize 0 as the starting point, there are 3 gray boxes that are not used as shown (highlighted in the red box) in the pic? Are these boxes to show that they are gaps or just to align them properly?
Heeh wei cheng
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How to output all sequences with bwa mem, not `*`?

I've been running bwa mem -a for alignment, using the -a flag---this will output all alignments for SE or unpaired PE I've noticed in the SAM that there are several alignments with * in the SEQ and QUAL fields. Based on the documentation: SEQ:…
EB2127
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