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We are close to releasing our new pipeline schema which describe input parameters. Through chatting to people at BOSC 🍐 I've become aware of a project called [Bioschemas](https://bioschemas.org) which…
ewels updated
3 years ago
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Hey folks, big fans of starcode. I really like this tool (well designed, Levenshtein distance, code is readable), and I'd like to use it for all my seq clustering needs. I hope y'all are continuing ac…
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Hi all,
I am using align_trim.py script to remove primers from the alignment. In me case, we have performed SARS2 amplification with v3 primer set, and then sequenced with illumina (Miseq).
I …
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We need to do a bead size selection clean up to remove primer dimers from our pooled PCR product for ITS2. Details of the amplification and prep for these samples are in my [notebook post](https://ahu…
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Dear,
I find the ANCOM-BC approach to identify deferentially abundant taxa very interesting and was wondering if the estimated sample-specific offset term could be replaced by a known sampling frac…
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I am analyzing ITS1 amplicon data using DADA2 and the UNITE reference database. Last week I had an issue where the assignTaxonomy function was labeling ASVs as outlandish taxa (telling me I had marine…
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VPIPE_BASEDIR = /opt/V-dock/V-pipe/workflow
Importing legacy configuration file vpipe.config
MissingSectionHeaderError in line 107 of /opt/V-dock/V-pipe/workflow/rules/common.smk:
File contains no …
dstcr updated
2 years ago
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**Submitting author:** @jinfinance (Rong Jin)
**Repository:** https://github.com/ncezid-biome/HMAS-QC-Pipeline2
**Branch with paper.md** (empty if default branch): main
**Version:** v1.2.0
**Editor:**…
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Hello,
I have followed the BaitSTR workflow to create 'contigs.str.fa' for one of my datasets. I am now trying to use BaitSTR_type and it looks to be getting hung up on creating an index. I think …
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Hello,
I have a dataset sequenced with Novaseq 6000 with 250PE for 77 libraries and four primers: 12S, COI, ITS and 18S, which gave ~1-6 million paired reads per library, with some lower exceptions…