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Recent Replies
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
shevch2009
▴
20
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
by
GenoMax
153k
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
by
shevch2009
▴
20
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
by
ramiro.barrantes
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60
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
by
shevch2009
▴
20
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
by
GenoMax
153k
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
by
colindaven
7.8k
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, …
Comment: Low Mapping Rate with Kallisto on RNA-seq Data
by
GenoMax
153k
> 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 …
Comment: Low Mapping Rate with Kallisto on RNA-seq Data
by
Buffo
★
2.4k
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
by
ATpoint
89k
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…
Comment: Feedback needed on new user-friendly BED file tool
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ATpoint
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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…
Comment: Low Mapping Rate with Kallisto on RNA-seq Data
by
ATpoint
89k
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
by
GenoMax
153k
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…
Comment: What is the difference between agilent_wholegenome and agilent_wholegenome_4x44k
by
Jacob
•
0
You’ve got a small typo in your second check:
# was:
table(wg$agilent_wholegenome %in% wg44v1$agilent_wholegenome_4x44k_v2)
…
Comment: RNAseq requirements: Biological and Technical replicates
by
jkim
▴
220
I don't think technical replicates are not necessary.
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