Highest Voted Questions - Bioinformatics Stack Exchange

7

votes

1 answer

Density plot, scale it to 0-1

Doubt regarding density plot what is the scale being plotted in the Y axis.Is it possible to scale it to 1?. This is my code w <- read.csv("Normal_Myeloid_Dev_stages/Myeloid_non_coding_non_CDS_CORRVALUE.txt",header = TRUE) head(w) #names(w)[1] =…

asked Dec 16 '19 at 17:26

kcm

1,804
12
27

7

votes

1 answer

How to interpret contig-alignment.psa produced by velvet

I'm using velvet to align given reads of RNA to given CDSs (i.e. coding areas and genes) of an organism, so I can generate gene-expression profiles. But after using velvetg out-dir/ -alignment yes, velvet produces contig-alignment.psa which is a…

asked Jul 08 '17 at 13:35

hhoomn

325
1
5

7

votes

1 answer

scanBam from Rsamtools is not importing one of my reads into R

I have this read in my BAM file. It maps on chromosome 1. I open this BAM file in IGV, and I can see the alignment on chromosome 1. But when I open this file in R with Rsamtools: bamContigsCel <- Rsamtools::scanBam('output/alignment/pacbio/bwa/ref …

asked Jul 07 '17 at 10:02

Biomagician

2,459
16
30

6

votes

2 answers

Human body sites knowledge base

I'm looking for a lightweight knowledgebase describing the human body to annotate disease sites. I do not need a great level of detail, I just need a kind of basic organs/sub-organs taxonomy. I checked out the Foundational Model of Anatomy…

asked Jul 05 '17 at 15:23

floatingpurr

315
1
2
7

6

votes

3 answers

Calculating the charge of a peptide computationally

I was wondering how I can calculate the charge of a protein peptide (e.g. "RKTTLVPNTQTASPR") computationally in R or another tool.

asked Jul 04 '17 at 12:53

J. Doe

575
3
11

6

votes

1 answer

PASA pipeline: compare experimental transcripts to the reference annotation

I would like to ask if anyone has experience in running a subset of the PASA pipeline, in particular for the reconciliation of some experimental 'transcripts' with the reference annotation. In more detail, I am working with RNA-seq data from D.…

asked Jul 03 '17 at 09:09

aechchiki

2,676
11
34

6

votes

2 answers

Is there any way of using biopython to write Swissprot files?

I have the following mwe for filtering a Swissprot file based on a certain feature, in this case, transmembrane regions. from Bio import SeqIO records=[] for record in SeqIO.parse("Input.txt", "swiss"): transmembrane_protein=False print…

asked Jun 29 '17 at 08:58

James

409
2
13

6

votes

1 answer

How to find hairpin loop structure in a large set of long non coding RNA transcripts

I have done de novo assembly of pair end raw read sequences and resulted transcripts sequences were separated based on coding potential into two categories: long non-coding RNA transcripts and coding RNA transcripts. I want to find how many of long…

asked Jun 29 '17 at 08:42

bioinfonext

393
2
14

6

votes

1 answer

What are the labels in my rstats distance matrix?

I have a distance matrix generated by hierfstat, thusly, with a link to the fasta file here: library(adegenet) library(hierfstat) snps <- fasta2DNAbin('test.fa', chunkSize = 50) gi <- DNAbin2genind(snps) # manually define the populations for passing…

r

asked Jun 28 '17 at 05:28

flashton

217
2
6

6

votes

2 answers

Running differential expression analyses on count matrices with many zeroes

Note: I also posted this issue (with less context) in the bioconductor support site: https://support.bioconductor.org/p/97424/ I'm working on a snakemake workflow that identifies various small RNA species in C. elegans small RNA-seq libraries. Some…

asked Jun 26 '17 at 09:14

bli

3,130
2
15
36

6

votes

1 answer

How can I translate infix to mathml using the python interface to libsbml?

Assume I have an infix expression such as k1*s1, how do I use libsbml to translate this expression to mathml using the python interface?

asked Jul 18 '19 at 08:58

rhody

251
1
6

6

votes

1 answer

Convert BAM to properly paired FASTQ files

I thought I had figured this one out. But apparently not. I need to convert a BAM file of paired-end alignments to two FASTQ files of paired reads to realign them, with a twist: I only want reads that fall within a defined region. Currently I am…

asked Jul 09 '19 at 11:22

Konrad Rudolph

4,845
14
45

6

votes

1 answer

How to maximize fastq parsing with FastqGeneralIterator (Bio.SeqIO.QualityIO)

I'm contributing to a python-based project that uses Biopython to analyze fastq files. It currently uses SeqIO.parse, which populates various structures with all of the fastq information (including converting quality scores). There is apparently a…

asked Jun 22 '17 at 23:42

Mark Ebbert

1,354
10
22

6

votes

1 answer

How does MinKNOW classify 1D reads as "pass" or "fail"?

I have found a couple of sources1,2 that indicate that a read in a 1D² run is classified by MinKNOW as "pass" and put into the fastq_pass folder if both of the following conditions are met: Both strands were read The average Phred score of all…

asked May 31 '19 at 11:19

Mark Amery

277
2
13

6

votes

1 answer

Determine reference for reference-compressed SRA file

Note: this question was also asked on Github. I have 241 SRA files that appear to be reference compressed. I didn't even know this was a thing until I tried to convert them to Fastq files without an internet connection. I got the "name not found…

asked May 14 '19 at 19:10

Daniel Standage

5,080
15
50

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