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Recent Replies
Answer: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
LChart
5.0k
I have used BURST (https://github.com/knights-lab/BURST) to do this before. You can take fastA sequences for your target genes and build ou…
Comment: RNAseq requirements: Biological and Technical replicates
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Ram
45k
Why not just say "technical replicates are necessary"?
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
shevch2009
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Well, we already have mags, but my boss want to check the raw reads, that is why I am trying to find a way.
Well, human got me errors, it…
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
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GenoMax
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Then you need to decide if you want to assemble your reads into contigs/MAG's followed by using the tools discussed. Or do the mapping usin…
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
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shevch2009
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I considered mapping the reads to a database, but that approach wouldn't provide the gene names or the metabolic pathways the genes partici…
Comment: Criteria for choosing variants
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ramiro.barrantes
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Thank you. It has not been my understanding or experience that calling variants in tumor-normal pairs is straightforward, especially somati…
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
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shevch2009
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I don't think any kind of web-based tool will work; the read files are very large (at least 10 GB). Usually, web versions have restrictions…
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
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GenoMax
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A quick look suggests that this tool is expecting longer sequences (if the example is to go by in sequence search) that need to be protein …
Answer: Tools for raw reads that estimate the percentage of reads that hit marker genes
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colindaven
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I believe **Mgnify** at the EBI https://www.ebi.ac.uk/metagenomics does something like this for you using domains. But I have not used it, …
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> I checked for contamination using fastq_screen, and most of the reads (>90%) mapped to human genome on a subset of 2M reads.
Looks like …
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Buffo
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Kallisto is a pseudoaligner, so, as @atpoint suggested, it could be DNA contamination. You can confirm this using an aligner and a referenc…
Comment: RNAseq requirements: Biological and Technical replicates
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ATpoint
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What is a technical replicate to you? A repeated library prep on the same pool of RNA? If so then no, I don't see the point as downstream a…
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What I said already: Don't reimplement, wrap existing tools. I just tried some corrupted files (malformatted), and it threw no errors. It s…
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ATpoint
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Could be genomic DNA contamination. Enrichment is just that, enrichment, not perfect selection without noise. Poor RNA quality usually incr…
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
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Only one of the files should be enough to give you an idea of what that fragment (read-pair) likely is from, which is what you seem to want…
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