Questions tagged [indexing]

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4 votes
1 answer
67 views

Can index hopping lead to more reads in samples?

We run multiple samples for sequencing on an Illumina NovaSeq machine. After converting the files to fastq format using bcl2fastq, we can see that we have some ...
1 vote
0 answers
44 views

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
29 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
133 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
4k 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
266 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
490 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 ...
5 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 ...