bioinformatics Questions
4
Solved
QIIME requests this (here) regarding the fasta files it receives as input:
The file is a FASTA file, with sequences in the single line format. That is, sequences are not broken up into multiple li...
Cheryllches asked 11/6, 2014 at 7:1
12
Solved
I have a DNA sequence and would like to get reverse complement of it using Python. It is in one of the columns of a CSV file and I'd like to write the reverse complement to another column in the sa...
Gat asked 7/8, 2014 at 17:50
4
Solved
I would like to extract sequences from the multifasta file that match the IDs given by separate list of IDs.
FASTA file seq.fasta:
>7P58X:01332:11636
TTCAGCAAGCCGAGTCCTGCGTCGTTACTTCGCTT
CAAGTC...
Kalin asked 9/4, 2018 at 11:1
5
Solved
I have a small fasta file of DNA sequences which looks like this:
>NM_000016 700 200 234
ACATATTGGAGGCCGAAACAATGAGGCGTGATCAACTCAGTATATCAC
>NM_000775 700 124 236
CTAACCTCTCCCAGTGTGGAACCTCTAT...
Glossectomy asked 21/1, 2014 at 16:23
4
Solved
I'm trying to merge multiple .bed files by identifying the first two columns chr and start following this,
Merging multiple files with two common columns, and replace the blank to 0
However, I'm wo...
Dental asked 29/1 at 4:58
5
Solved
I have this file:
m64071_220512_054244/12584899/ccs rev pet047-10055 ACGTGCGACCTTGTGA TTGAGGGTTCAAACGTGCGACCTTGTGA
m64071_220512_054244/128321000/ccs rev pet047-10055 ACGTGCGACCTTGTGA TTGAGGGTTCAAA...
Nerta asked 21/12, 2023 at 19:24
5
Solved
I have a dataframe of expression data where gene are rows and columns are samples. I also have a dataframe containing metadata for each sample in the expression dataframe. In reality my expr datafr...
Nepotism asked 21/12, 2023 at 18:6
3
Solved
I'm currently working on a bioinformatics project using R, and I'm encountering an error when trying to use the biomaRt package. After installing the package and loading it into R, I tried to selec...
Coburg asked 26/10, 2023 at 22:45
5
I have a Fortran program and want to execute it in python for multiple files. I have 2000 input files but in my Fortran code I am able to run only one file at a time. How should I call the Fortran ...
Gael asked 3/3, 2017 at 6:58
2
I was looking in the wiki how to convert the following information about beads, cartesian coordinates + energy :
23.4 54.6 12.3 -123.5 54.5 23.1 9.45 -56.7 .......
to a draw in pymol that contain...
Lally asked 13/1, 2010 at 21:57
2
Solved
I am working on a rather complex snakemake workflow that spawns several hundreds of thousands of jobs. Everything works... The workflow executes, DAG gets created (thanks to the new checkpoint impl...
Garnishment asked 28/2, 2019 at 9:49
14
Solved
I have a data in that always comes in block of four
in the following format (called FASTQ):
@SRR018006.2016 GA2:6:1:20:650 length=36
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN
+SRR018006.2016 GA2:6:1:20...
Raddle asked 9/10, 2009 at 7:22
3
Solved
I have a data.frame containing Ensembl IDs in one column; I would like to find corresponding gene symbols for the values of that column and add them to a new column in my data frame.
I used bioMaRt...
Pelops asked 16/2, 2015 at 14:22
3
I am trying to find a way to collapse rows with intersecting ranges, denoted by "start" and "stop" columns, and record the collapsed values into new columns. For example I have this data frame:
my...
Consignee asked 6/6, 2013 at 8:33
3
Solved
I have this VCF format file, I want to read this file in R. However, this file contains some redundant lines which I want to skip. I want to get something like in the result where the row starts wi...
Changeful asked 11/9, 2015 at 0:45
11
Solved
I am trying to pass BioPython sequences to Ilya Stepanov's implementation of Ukkonen's suffix tree algorithm in iPython's notebook environment. I am stumbling on the argparse component.
I have ne...
Uroscopy asked 5/6, 2015 at 1:12
4
Solved
I was wondering if there is a way to have optional inputs in rules.
An example case is excluding unpaired reads for alignment (or having only unpaired reads). A pseudo rule example:
rule hisat2_a...
Turnbow asked 16/7, 2018 at 12:47
7
As preparation for an upcoming bioinformatics course, I am doing some assignments from rosalind.info. I am currently stuck in the assignment "Mendel's First Law".
I think I could brute force mysel...
Canton asked 4/8, 2014 at 12:50
4
I'm trying to solve the problem at http://rosalind.info/problems/iprb/
Given: Three positive integers k, m, and n, representing a population
containing k+m+n organisms: k individuals are homozy...
Smoothshaven asked 15/10, 2014 at 15:10
4
Solved
I have a pandas dataframe that looks as the following one:
chrom start end probability read
0 chr1 1 10 0.99 read1
1 chr1 5 25 0.99 read2
2 chr1 15 25 0.99 read2
3 chr1 30 40 0.75 read4
What I ...
Clicker asked 12/2, 2018 at 18:13
3
Solved
Unambiguous DNA sequences consist only of the nucleobases adenine (A), cytosine (C), guanine (G), thymine (T). For human consumption, the bases may be represented by the corresponding char in eithe...
Hereditament asked 9/1, 2022 at 8:28
14
FYI: this is NOT a duplicate!
Before running my python code I installed biopython in the cmd prompt:
pip install biopython
I then get an error saying 'No module named Bio' when try to import i...
Viscometer asked 16/4, 2018 at 1:33
3
I am using python/pysam to do analyze sequencing data. In its tutorial (pysam - An interface for reading and writing SAM files) for the command mate it says:
'This method is too slow for high-thro...
Chokefull asked 16/12, 2015 at 1:37
4
Solved
I was curious to know if there is any bioinformatics tool out there able to process a multiFASTA file giving me infos like number of sequences, length, nucleotide/aminoacid content, etc. and maybe ...
Mitchiner asked 24/11, 2009 at 10:55
1
Solved
I have a dataset in R that is a class of 'Formal class enrichResult'. I plot the genes in this dataset using cnetplot() from the package DOSE - which is meant to be based on ggplot graphics. This p...
About asked 9/9, 2021 at 16:45
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