All Questions
5,572
questions
3
votes
1
answer
483
views
How to extract exome on-target reads in batch?
I was given a list of target regions in BED and many exome alignments in BAM. I was asked to extract on-target alignments from these BAMs to save disk space. I know I can use bedtools to extract sub-...
- 777
4
votes
3
answers
375
views
Is spark widely used in bioinformatics?
I learned that GATK 4 is using Spark for parallelization. I googled around, though I am still not quite sure how spark really works and how to use it in practice. Besides GATK 4, are any other ...
- 777
6
votes
1
answer
140
views
What is the difference between SAM mapping quality and Blast E-value?
Blast reports E-values, but short-read mappers report mapping qualities. Are they the same thing? Can they be converted to each other? If not, why blast doesn't report mapping quality while short-read ...
- 777
7
votes
3
answers
1k
views
What is the difference between NGS, 2GS, SBS and HTS?
I've come across a bit of confusion about the initialism NGS, so think it would be a good idea to clarify this term (and similar terms like 2GS, SBS, and HTS) for this site with a bit of discussion.
...
- 13k
15
votes
1
answer
4k
views
Why is bwa-mem the standard algorithm when using bwa?
The industry standard for aligning short reads seems to be bwa-mem. However, in my tests I have seen that using bwa backtrack (bwa-aln + bwa-sampe + bwa-samse) performs better. It is slightly slower, ...
- 9,352
7
votes
3
answers
805
views
Merging sequencing data for ChIP-seq experiments
I need to merge sequencing data from different sequencing runs but for the same ChiP-seq library (HiSeq 2000).
Are there any potential advantages or disadvantages when merging files at .fastq or .BAM ...
- 481
17
votes
5
answers
4k
views
What's the best way to download data from the SRA? Is it really this slow?
I'm trying to download three WGS datasets from the SRA that are each between 60 and 100GB in size. So far I've tried:
Fetching the .sra files directly from NCBI's ftp site
Fetching the .sra files ...
- 171
5
votes
1
answer
229
views
Do you use SNAP for short-read mapping?
I am calling SNPs from WGS samples produced at my lab. I am currently using bwa-mem for mapping Illumina reads as it is recommended by GATK best practice. However, bwa is a bit slow. I heard from my ...
- 777
6
votes
1
answer
578
views
Why most aligners do not output the "X" CIGAR operation?
As I read the SAM spec, the "X" CIGAR operator represents a mismatch. This seems useful as we can know where are the mismatches without looking at the reference genome. However, many popular aligners ...
- 777
15
votes
1
answer
4k
views
What is the difference between samtools, bamtools, picard, sambamba and biobambam?
After some google searches, I found multiple tools with overlapping functionality for viewing, merging, pileuping, etc. I have not got time to try these tools, so will just see if anyone already know ...
- 777
18
votes
3
answers
13k
views
How can I downsample a BAM file while keeping both reads in pairs?
I know how to downsample a BAM file to lower coverage. I know I can randomly select lines in SAM, but this procedure can't guarantee two reads in a pair are always sampled the same time. Is there a ...
- 777
9
votes
2
answers
1k
views
Why do BAM files created by different tools have different file sizes?
I have a BAM created by Picard. I want to filter alignments by flags with samtools view. However, I noticed that even if I apply no filters, the output BAM is ...
- 777
8
votes
1
answer
3k
views
What are all the reference files produced by bwa index, and are these dependent upon whether the reference is zipped?
I have indexed a gzipped reference with bwa: bwa index reference.fa.gz, which produces a series of other files ...
- 744
6
votes
2
answers
179
views
validating identified sub-populations of cells in scRNA-seq
In the analyses of single-cell RNA-seq data there are different unsupervised approaches to identify putative subpopulations (e.g. as available with Suerat or SCDE packages).
Is there a good way of ...
- 153
13
votes
6
answers
382
views
Are there any databases of templates for common bioinformatic file formats?
I want some templates of different file formats that I can use to test my scripts and identify possible bugs in my code.
For example, consider nucleotide FASTA, a simple but often abused format, I ...
- 3,858
14
votes
3
answers
317
views
Generic HMM solvers in bioinformatics?
Hidden Markov models (HMMs) are used extensively in bioinformatics, and have been adapted for gene prediction, protein family classification, and a variety of other problems. Indeed, the treatise by ...
- 5,010
14
votes
2
answers
410
views
Finding the location and unit length of repetitive sequences within a long read
After discovering a few difficulties with genome assembly, I've taken an interest in finding and categorising repetitive DNA sequences, such as this one from Nippostrongylus brasiliensis [each base is ...
- 13k
7
votes
2
answers
534
views
Missing genes and normalisation of RSEM output using EBSeq
Without going into too much background, I just joined up with a lab as a bioinformatics intern while I'm completing my masters degree in the field. The lab has data from an RNA-seq they outsourced, ...
- 541
20
votes
3
answers
7k
views
How exactly is "effective length" used in FPKM calculated?
According to this famous blog post, the effective transcript length is:
$\tilde{l}_i = l_i - \mu$
where $l_i$ is the length of transcript and $\mu$ is the average fragment length. However, typically ...
- 6,295
20
votes
10
answers
6k
views
What is the fastest way to calculate the number of unknown nucleotides in FASTA / FASTQ files?
I used to work with publicly available genomic references, where basic statistics are usually available and if they are not, you have to compute them only once so there is no reason to worry about ...
- 5,467
9
votes
5
answers
1k
views
Using shells other than bash
As someone who's beginning to delve into bioinformatics, I'm noticing that like biology there are industry standards here, similar to Illumina in genomics and bowtie for alignment, many people use ...
- 483
8
votes
3
answers
1k
views
Tumor purity/contamination/admixture estimation
Can anyone recommend a good tool for estimating the tumor content given a matched tumor and normal file for DNA NGS whole genome sequencing data or whole exome data?
Is it possible to estimate this ...
- 83
12
votes
2
answers
326
views
How to select high quality structures from the Protein Data Bank?
Models of structures deposited in the Protein Data Bank vary in the quality, depending both on the data quality and expertise and patience of the person who built the model. Is there a well-accepted ...
- 1,176
13
votes
1
answer
4k
views
What's the difference between VCF spec versions 4.1 and 4.2?
What are the key differences between VCF versions 4.1 and 4.2?
It looks like v4.3 contains a changelog (specs available here) but earlier specifications do not.
This biostar post points out one ...
- 356
19
votes
6
answers
3k
views
Are there any RepBase alternatives for genome-wide repeat element annotations?
I’m using the RepBase libraries in conjunction with RepeatMasker to get genome-wide repeat element annotations, in particular for transposable elements.
This works well enough, and seems to be the de ...
- 4,815
6
votes
0
answers
725
views
Difference between computational biology, bioinformatics and biostatistics [closed]
I find that in many contexts, the terms computational biology, bioinformatics and biostatistics are often treated as functionally equivalent, and yet for students selecting PhD programs and the like ...
- 2,123
7
votes
1
answer
165
views
Imputing missing genotypes from separate genotyping panels
What is the current standard for imputing missing genotypes between two genotyping panels? I have two populations genotyped using two different panels (A & B), and I would like to impute all the ...
- 841
4
votes
2
answers
332
views
How to calculate statistical significance of sequence motifs
I would like to show that certain types of RBP motifs are enriched in RNA editing islands (i.e. clusters of RNA editing). However, I am unsure about how to think about sequence motifs with respect to ...
- 171
6
votes
2
answers
155
views
Structural variant calling for low-coverage PacBio data
PacBio is selling ~10x PacBio SEQUEL long reads as an upgrade to Illumina data for SV discovery.
In a clinical setting, the main requirements are proper sensitivity and specificity but also the ...
- 588
6
votes
1
answer
114
views
Stable download URLs
One big problem that I'm regularly facing is that URLs for downloading Bioinformatics data (e.g., RefSeq releases or NCBI genome releases) disappear.
Does anyone have any good solution for this?
- 588
5
votes
5
answers
609
views
QC measures for NGS sequencing
What are good means for performing quality control (QC) or NGS reads?
I'm aware of:
FastQC
NGS Screen
Kraken (e.g., for screening against contaminants)
What are other popular means for such QC?
- 588
3
votes
3
answers
85
views
Which reference to use for read mapping for popular model organisms
What is the "best" assembly for the popular model organisms:
human (GRCh37 and GRCh38 are obvious, I'd pick whatever bwakit uses)
mouse (GRCm37/GRCm38, OK)
but what about non-human/mouse ones?
...
- 588
15
votes
2
answers
11k
views
Downloading a reference Genome for Bowtie2
How do I download a reference genome that I can use with bowtie2? Specifically HG19. On UCSC there are a lot of file options.
- 483
8
votes
4
answers
1k
views
Is there a point in recalibration of scores for variant calling?
The most variant calling pipeline GATK include a Base Quality Score Recalibration (BQSR) which requires a list of known variants. Recently, some work has been done for reference-free recalibration of ...
- 5,467
8
votes
4
answers
151
views
Working with old genome builds
Is working with and relying on old genome builds still valid?
For example NCBI36/hg18. Would results from papers based on old builds require LiftOver and re-analysis to be useful?
A bit of context, ...
- 1,042
6
votes
1
answer
206
views
Filtering imputed GWAS SNPs based on a MAF difference of 10%
There are many posts on the web regarding QC steps pre and post-imputation.
Does applying below (new?) 10% MAF difference rule make sense, pitfalls?
Here is the process:
Get MAF for imputed set, ...
- 1,042
3
votes
1
answer
43
views
How do I validate a single sample ArrayCGH result?
We have arrayCGH (aCGH) results for one sample. There is a 0.5 Mb terminal duplication on chromosome 19 (62995490-63407936, according to NCBI36/hg18). The duplication is rare: a literature review ...
- 1,042
6
votes
1
answer
117
views
Gene set enrichment analysis on differential phosphorylation sites
I have:
A list of differentially phosphorylated sites in a knockout condition. Some genes contain as many as 70 possible phosphorylation sites; others contain only one.
A list of genes belonging to a ...
- 191
5
votes
1
answer
453
views
Why is SMALT better for microbial genomics than other mappers?
SMALT seems to be one of the most used read mappers for bacterial data, see, e.g., this query. I do not say that it is not a great mapper, but I cannot easily see what are its main strengths compared ...
- 1,899
11
votes
1
answer
2k
views
Changing the record id in a FASTA file using BioPython
I have the following FASTA file, original.fasta:
>foo
GCTCACACATAGTTGATGCAGATGTTGAATTCACTATGAGGTGGGAGGATGTAGGGCCA
I need ...
- 481
5
votes
1
answer
215
views
Rapid metagenomics classifiers on long read data [closed]
I recently used the minION (Nanopore, 9.4 flow cell, RAD001 kit) to generate a metagenome out of environmental samples.
Passed reads weren't brilliant (196, average 1,594bp lenght), but working with ...
- 161
9
votes
2
answers
478
views
How to transfer gff annotations in genome with extensive duplications?
Microbial genomes can contain extensive duplications. Often we'd like to transfer annotations from an annotated species to one that is newly sequenced.
Existing tools (e.g. RATT, LiftOver, Kraken) ...
- 91
7
votes
2
answers
353
views
Which tools can detect chimeric RNA (fusion genes) from WGS or RNA-Seq data?
Given WGS data or RNA-seq data, which tools can I use to detect gene fusions?
- 281
12
votes
4
answers
900
views
How can I systematically detect unknown barcode/adapter sequences within a set of samples?
I have often downloaded datasets from the SRA where the authors failed to mention which adapters were trimmed during the processing.
Local alignments tend to overcome this obstacle, but it feels a ...
- 1,568
14
votes
3
answers
1k
views
How can I improve the yield of MinION sequencing runs?
This is a frequently-asked question within the nanopore community. Oxford Nanopore currently claims that they are able to generate run yields of 10-15 gigabases (e.g. see here and here), and yet it's ...
- 13k
13
votes
2
answers
3k
views
Is it possible to perform MinION sequencing offline?
I vaguely remember, that the original plan of Oxford Nanopore was to provide cheap sequencers (MinION), but charge for base-calling. For that reason the base-calling was performed in the cloud, and ...
- 2,715
14
votes
1
answer
4k
views
How does the BWA-MEM algorithm assign its mapping qualities?
Is there any resource (paper, blogpost, Github gist, etc.) describing the BWA-MEM algorithm for assigning mapping qualities? I vaguely remember that I have somewhere seen a formula for SE reads, which ...
- 1,899
8
votes
3
answers
164
views
Have DNA motifs 6-12bp long, trying to get conservation scores
I have about 200 short nucleotide motifs (6-12 bp in length) from the human genome, and I'm trying to see how conserved they are across vertebrates.
I was thinking that I'd need to make a bed file ...
- 133
13
votes
2
answers
354
views
Remapping genomic coordinates to account for indels
I'm interested in obtaining coding sequences of my favourite gene in all individuals from the 1000Genomes (and similar projects). I use GATK to get the right subset of variants, vcf-consensus to map ...
- 232
5
votes
3
answers
1k
views
Is there any publicly available multi-omics dataset?
I am searching for a multi-omics dataset which may include genomics, transcriptomics and proteomics (eg. snyderome).
I need such a dataset for an introductory data-exploration purpose. So it can be ...
- 665