Bioinformatics Stack Exchange
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Finding URL for UCSC data hub

I am trying to build a UCSC track hub (a private one). I have all my hub files on a university server in a simple folder called /hub. I am using Ubuntu 16.04 and the server is also Ubuntu (16.04.3 LTS (GNU/Linux 4.4.0-98-generic x86_64). I have…
mf94
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Why is cell count stated relative to animal size?

Why do some single-cell RNA-seq papers give the number of cells sampled as a fraction of the size of the organ, animal, or embryo, as opposed to just saying how many cells they sampled? For instance, Wagner et al.'s paper "Single-cell mapping of…
eric_kernfeld
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Why DoHeatmap Does not show all genes in genes.use?

I am heatmaping a list of genes by DoHeatmap function in Seurat R package. I am sure I have 212 genes but heat map shows only a few of my genes > DoHeatmap( + object = seurat, + genes.use = genes, + slim.col.label = TRUE, + …
Zizogolu
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Do people today with a disease caused by single gene mutation that is inheritable - all share a common ancestor?

First question here so sorry if it is about both genetics and evolution. So, if I get a disease which can be clearly identified on the gene level and all my descendants inherit it, after 500 years do all people with the disease share the common…
Perf Lar
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How to map reads shorter than 32bp with minimap2?

I mapped fasta sequences to a reference. The fasta sequences range in length from 17bp up to several hundred bp. I used minimap2 with the following command: minimap2 -ax sr ref.fa seqs.fa, et cetera. Only the sequences greater than 32bp len mapped…
conchoecia
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how to filter out cell after doing QC

I was wondering that the threshold that we set after doing QC in Seurat. there is an example # GenePlot is typically used to visualize gene-gene relationships, but can be used for anything # calculated by the object, i.e. columns in…
hua
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1 answer

Glocal\semi-local\Hybride Globale-Local alignment with Python

I was looking for a simple way to do a glocal alignment. The case I have is I have a small sequence which should be find in a bigger one, thus typically a glocal alignment. Also I can not Install anything on the target machine (Python 3.6 with…
Ckln
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RNA-Seq type and and optimal fusion detection

There are several popular types of RNA-Seq library prep which are frequently used: total RNA (with and without ribosomal depletion), mRNA-Seq/poly-A, and targeted mRNA-Seq/RNA exome. What would the impact of choice of these various types of RNA-Seq…
Matt Bashton
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1 answer

Path to career in bioinformatics?

I've been completing various courses on bioinformatics through edX and Coursera, and I've made a strong footing in the material. I'm not sure what to pursue next in bioinformatics that would bring me closer to research in the field or employment.…
Rock910
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Hemoglobin subunits genes in scRNA-seq

In one scRNA-seq sample I encountered the genes: Hbb-bs, Hba-a1 and Hba-a2. These genes appear on top of the list of the highest expressed genes but the 75% percentile of cells have very low counts. Therefore the expression is highly…
gc5
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How to assess the quality of assembled .fasta genome files?

I have assembled 3 .fasta files from contigs infastq format of 3 different Homo sapiens. I would like to see if the assembled genomes which are in .fasta format are in good quality or not. In addition, I would be happy to see heritages of genes…
0x90
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The algorithm behind makeblastdb?

What is the algorithm/concept behind‚makeblastdb? I know makeblastdb produces a .phr, .pin, and a .psq file, that represents an index or a data structure that is better optimised for searching a given query. What is exactly stored in these…
Paul
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Change sample names while using cummeRbund

I want to analyze RNA seq data using R package cummeRbund. Using this package I have a problem changing sample names. When I run this command in cummeRbund samples(cuff) sample_index sample_name sample_name parameter value 1 1 …
Ammar Sabir Cheema
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3 answers

Annotation with Prokka or RAST

I was experimenting Prokka and RAST annotation tools. So, I took a well-annotated swinepox virus genome from genebank (NCBI Reference Sequence: NC_003389.1). I ran those sequences on Prokka and RAST Seed server at the same time. I can see that only…
L R Joshi
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How to visualize genome track of gene in specific cell-lines?

I'm trying to make a plot showing genome tracks of specific genes in specific cell-lines of RNA-seq and Chip-seq data. It should look something like this I have recently seen this encode, but in this I didn't find any MDAMB231 cell-lines. May I…
stack_learner
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