Questions tagged [indexing]
The indexing tag has no usage guidance.
10
questions
2
votes
1
answer
26
views
Is it possible to, all in memory without writing a file, given a list of AlignedSegments and a bam header, build a bam, index and get coverage?
My current job is rate-limited chiefly by the IO overhead of writing reads to their corresponding bam files (they are split up by both cell barcode and contig). The only reason I need to write these ...
- 123
1
vote
1
answer
71
views
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 ...
- 11
0
votes
1
answer
3k
views
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 ...
- 103
1
vote
1
answer
225
views
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 ...
- 280
2
votes
2
answers
404
views
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 ...
- 335
3
votes
1
answer
7k
views
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 ...
- 189
6
votes
1
answer
2k
views
Index a BAM file using pysam
(How) can you index a BAM file using pysam?
When I tried the intuitive pysam.index I got:
...
- 5,517
2
votes
1
answer
234
views
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 ...
- 319
3
votes
2
answers
2k
views
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, ...
- 131
1
vote
4
answers
1k
views
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 ...
- 5,060