Questions tagged [indexing]

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1 vote
0 answers
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java.lang.ArrayIndexOutOfBoundsException: Index 86 out of bounds for length 86

I use the next versions: gatk 4.4.0.0 minimap2 2.26-r1175 samtools 1.19 I have a fastq file. And try to implement gatk MergeBamAlignment to generate a new ...
6 votes
1 answer
3k 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: ...
2 votes
1 answer
28 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 ...
1 vote
1 answer
114 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 ...
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 ...
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 ...
1 vote
1 answer
242 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 ...
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, ...
2 votes
2 answers
456 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 ...
4 votes
1 answer
8k 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 ...
2 votes
1 answer
237 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 ...