Questions tagged [software-recommendation]

Questions asking whether a software exists for a certain purpose; questions asking which software is best among a selection for a certain purpose.

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12
votes
4answers
4k views

How to convert BED to GFF3

I would like to convert a BED format to GFF3. The only useful tool that I could find via a google search seems to be Galaxy, ...
2
votes
0answers
67 views

ngs time course experiment [duplicate]

I have a question regarding the RNA-Seq analysis. We have a time course data regarding a mouse model wt and mutant treated with a drug (10uM) and the taken down at different time points: 8 time ...
6
votes
3answers
209 views

Visualization tools for 3C/Hi-C long-range interaction data?

I have identified a genomic region (CpG island) that is enriched for a characteristic of interest in the vast majority of my samples. After viewing it in the UCSC genome browser, I have confirmed ...
9
votes
2answers
2k views

How to convert GFF3 to GTF2

I would like to convert a file in gff3 format to a gtf2.2 format. The reason why I would like to do this is: I have a set of ...
6
votes
2answers
375 views

What tools can I use for a bacterial core/pan genome pipeline?

I want to perform a genome comparison on a group of isolates. I want to look into two broad groups of taxa and compare the accessory genome in each group. I have been using prokka (v1.12) and roary (...
6
votes
3answers
418 views

tools to reconcile experimental transcripts with reference annotation

Looking for tools to reconcile alignment file of experimental transcripts mapped to genome (SAM/BAM) with the reference transcriptome annotation (GTF) from Ensembl (organism: D. melanogaster). The ...
4
votes
2answers
321 views

Reordering scaffolds according to a reference without a genetic map

I am trying to reorder scaffolds of a rice species, but no genetic map is available right now. Oryza sativa Japonica is a close relative of this rice species. Mummer was used to do a whole genome ...
11
votes
8answers
10k views

Fast way to count number of reads and number of bases in a fastq file?

I am looking for a tool, preferably written in C or C++, that can quickly and efficiently count the number of reads and the number of bases in a compressed fastq file. I am currently doing this using <...
5
votes
1answer
70 views

How can I dock a protein to a nucleic acid?

I have a protein of interest and I would like to now how it interacts with RNA. I have structures of both molecules. What tool can I use?
10
votes
4answers
3k views

How do I generate a color-coded tanglegram?

I want to compare two phylogenies and colour the association lines based on some metadata I have. I have been using ape cophyloplot but I have not had any success in getting the lines to colour ...
4
votes
3answers
663 views

Analysis of differential transcript usage (DTU)

Recent breakthroughs in bioinformatics tools for quantification (e.g. Cufflinks/Kallisto/Salmon etc.) and tools which can identify differential transcript usage (DTU) (e.g. DRIMSeq, Cufflinks etc.) ...
7
votes
5answers
458 views

What motif finding software is available for multiple sequences ~10Kb?

I have around ~3,000 short sequences of approximately ~10Kb long. What are the best ways to find the motifs among all of these sequences? Is there a certain software/method recommended? There are ...
21
votes
4answers
650 views

Tools for simulating Oxford Nanopore reads

Are there any free open source software tools available for simulating Oxford Nanopore reads?

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