Questions tagged [indexing]

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5 votes
1 answer

Index a BAM file using pysam

(How) can you index a BAM file using pysam? When I tried the intuitive pysam.index I got: ...
Kamil S Jaron's user avatar
3 votes
2 answers

How to demultiplex a mix of single-indexed and dual-indexed samples

The problem If I have a sample sheet that contains both single-indexed and dual-indexed samples, I can split it up into two sample sheets and then run bcl2fastq on each one. However, when doing this, ...
AmadeusDrZaius's user avatar
2 votes
1 answer

Samtools Index: Chromosome Blocks not Continuous

I am working with short-read whole-genome sequences from the NCBI's SRA. I have aligned and sorted all of my short-read sequences and am attempting to index each sequence into .bai format using ...
annabelperry's user avatar
2 votes
2 answers

Get frequency of index sequences of fastq file

I recently did some sequencing on a MiniSeq and unexpectedly the Undetermined_S0_L001_R1_001.fastq.gz file contained quite a lot of data (about 40% of total). I ...
justinian482's user avatar
2 votes
1 answer

How to obtain file offsets corresponding to range query in block-gzipped file

How can we retrieve the file offsets of the zipped-chunks in a block-gzipped file that contain records for a region/window of interest (e.g. Chr01:100-Chr02:145)? It seems like the CLI of ...
init_js's user avatar
  • 319
1 vote
4 answers

Index VCF file for rapid access by rsID?

With tabix one can index a VCF file for rapid variant retrieval based on genomic position. I'm wondering if there are any tools that will index a VCF file to allow rapid retrieval using rsIDs and/or ...
Daniel Standage's user avatar
1 vote
1 answer

How to identify index sequences for cutadapt for atac-seq

I am just starting on my atac-seq analysis (not very experienced, so my apologies for a stupid question), and I am wanting to trim the adapters of off my paired-end reads. I am following the galaxy ...
Faleevs's user avatar
  • 11
1 vote
1 answer

How should I imagine the pre-indexing of suffix arrays in the STAR RNA Seq-aligner?

I'm using STAR for an internship (fusion-genes in ALL cancer) and I'd like to understand what exactly it is doing. The people at the internship don't know either how it works, given their biology ...
ilam engl's user avatar
  • 280
0 votes
1 answer

How to Sort and Index a SAM file without converting it to BAM?

Generally, I use samtools to sort and index BAM files. Samtools works also with BGZF ...
alec_djinn's user avatar