Github fgbio
WebDec 20, 2024 · fulcrumgenomics / fgbio Public Notifications Fork 55 Star 252 Code Issues 62 Pull requests 27 Actions Projects Wiki Security Insights New issue #557 Open fgvieira opened this issue on Dec 20, 2024 · 10 comments fgvieira on Dec 20, 2024 CorrectUmis converts all N s to A s GropuReadsByUmi allows variable length tags (hard) WebJun 19, 2024 · @yyren I believe you will need to run bcl2fastq with the --create-fastq-for-indexreads option to get FASTQs for the index reads. In this case, you should get four FASTQs assuming paired end reads and dual indexing: r1: reads from the first end of the pair; r2: reads from the second end of the pair; i1: reads from the first index read (no …
Github fgbio
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WebApr 2, 2024 · After picard, fgbio SetMateInformation, when I use ## fgbio-0.5.1.jar GroupReadsByUmi-s Adjacency, it broke. Like this: WebMar 10, 2024 · The paired method is intended for duplex sequencing applications where the two ends of the molecule (seen in R1 and R2 respectively) each contain a UMI and the UMIs are applied in such a way during library construction that the top and bottom strand of the same molecule end up with the same UMIs (albeit inverted between R1 and R2). From …
Webfgbio Metrics Descriptions fgbio fgbio Metrics Descriptions This page contains descriptions of all metrics produced by all fgbio tools. Within the descriptions the type of … Webfgbio is a command line toolkit for working with genomic and particularly next generation sequencing data. Getting Started Releases of fgbio are available from the GitHub …
Webfgbio 1.2.0: CallDuplexConsensusReads failed #631. Closed. alfonso-lam opened this issue on Sep 28, 2024 · 5 comments. WebAug 31, 2024 · The text was updated successfully, but these errors were encountered:
WebAug 23, 2024 · tfenne commented on Aug 23, 2024. @nicodemus88 It's a little hard to tell. GroupReadsByUmi discards reads for various reasons, the most common of which are that the read is not paired, or that the mapping quality is <= 30 (default), or that the read's mate pair is not aligned. The other requirement (listed in the usage) is that mapped pairs ...
WebAug 15, 2024 · I found an issue with the sort order of the DemuxFastq and the output of BWA. java -jar picard.jar SortSam I=DemuxFastq.bam O=QuerynameDemuxFastq.bam SORT_ORDER=queryname seems to do the trick. UPDATE, I also used Picard SortSam on the BWA aligned BAM to fix this issue. I have not tested this using the raw output (eg. … lawn mower lifetimeWebContribute to Yonghao-Holden/tricks development by creating an account on GitHub. lawn mower lift accessoriesWebfgbio/src/main/scala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala Go to file nh13 GroupReadsByUmi only sort input if it is not TemplateCoordinate sorted ( Latest commit a100106 on Mar 10 History 3 contributors 734 lines (640 sloc) 33.9 KB Raw Blame /** * Copyright (c) 2016, Fulcrum Genomics LLC * All rights reserved. * lawn mower lifespanWebFeb 20, 2024 · I am working with data that uses two UMIs for paired end reads. One UMI was included as part of index 1 and the other as part of index 2. I'd like to annotate the RX field in my BAM file with both UMIs with a dash between, as in NNNNNNNN-NNNNNNNN.I see that CorrectUmis can handle duplex UMIs, such that it looks for the consensus … lawn mower liftWebHi, I have a fastq data that have 8-bp UMI as the i5 index read. I read the instruction on FastqToBam has --extract-umis-from-read-names option. Could you give me an example of the read structure t... kamino flam heat shieldWebFeb 25, 2024 · Hi, There is no default value for min-base-quality in FilterConsensusReads, and I'm a bit unclear on the exact format of setting this, and also how consensus base qualities are encoded by CallMolecularConsensusReads. Is there an upper li... kaminoge the αWeb#!/bin/bash #!/usr/bin/awk # bash /bar/yliang/tricks/nanocage_pipe_v2.sh -f /scratch/yliang/HNSCC/data/nanocage_keratinocyte_rerun/fastq -a juheon lawn mower lifestyle stock