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12 votes
Accepted

Index a BAM file using pysam

Oh you silly sausage, pysam.index takes a bam file name, not a python object. ...
Kamil S Jaron's user avatar
7 votes
Accepted

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

Not only will you save disk space by converting to BAM, but BAM files are faster to manipulate than SAM. Source: Dave Tang's SAMTools wiki. sort supports ...
acvill's user avatar
  • 613
5 votes
Accepted

Samtools Index: Chromosome Blocks not Continuous

samtools sort blasted_SRR6649368.bam -o sorted_SRR6649368.bam -n These error messages indicate that the reads are not sorted by coordinate β€” in particular, that ...
John Marshall's user avatar
3 votes
Accepted

Can index hopping lead to more reads in samples?

The current best way to mitigate the effects of "index hopping" for short reads is to use dual / unique barcodes on each end of a sequenced library for each sample (as it appears you have ...
gringer's user avatar
  • 14.2k
3 votes
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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?

Assuming you are on an operating system that supports them, like Linux, you can try using named pipes in a ramdisk or tmpfs. Not the most elegant approach, but I don't know if what you are asking for ...
terdon's user avatar
  • 10.2k
2 votes

How to identify index sequences for cutadapt for atac-seq

The sequence to trim for ATAC-seq is CTGTCTCTTATACACATCT. It's the Nextera adapter sequence. The sequence is the reverse complement of the 3' ends of your primers, ...
ATpoint's user avatar
  • 1,326
2 votes

Index VCF file for rapid access by rsID?

I am not aware of any widespread index formats for query-by-QNAME for BAM or query-by-ID for VCF. I thought there were historical samtools{-devel,-help} threads to the effect of β€œin principle one ...
John Marshall's user avatar
2 votes

Index VCF file for rapid access by rsID?

high-perf-bio. I present my high-perf-bio project, which, for the most part, solves the problem of fast extraction of anything values from VCF, BED and unformatted data. Preparation. 1/ Run the ...
PlatonB's user avatar
  • 21
2 votes

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

So if the purpose of obtaining file offsets is to access subportions of remote files via protocols that samtools supports, as mentioned in this comment, then you can make your life easier and use ...
init_js's user avatar
  • 319
2 votes
Accepted

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

You can take a look at slide 40 of the lectures slides I use when I teach suffix arrays (reproduced here) An L-mer is a K-mer β€” STAR builds an explicit lookup table from all length 14 (by default) ...
nomad's user avatar
  • 472
1 vote
Accepted

Get frequency of index sequences of fastq file

I actually went back to the output folder on the MiniSeq and found this file: DemultiplexSummaryF1L1, which contains demultiplexing information of the whole run. ...
justinian482's user avatar
1 vote

Get frequency of index sequences of fastq file

I don't know that you can get them from that file. I've noticed that when the Miseq is left to run its version of fastq generation software, there are no indices in the undetermined file. I usually ...
swbarnes2's user avatar
  • 1,921
1 vote

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

I'm late to the party but simply run cellranger mkfastq twice, with different arguments for the mask and with --filter-dual-index...
plijnzaad's user avatar
  • 111
1 vote

Index VCF file for rapid access by rsID?

Take a look at grabix. Using grabix you could implement a binary search on a VCF sorted by rsID and compressed using ...
winni2k's user avatar
  • 2,286

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