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Recent Replies
Answer: ATAC-seq fragment size distribution - huge spike at 150 bp
by
yuntan1992
•
0
After removing adapters with trim_galore, change the parameter of bowtie2 " --local" to "--end-to-end".
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
shevch2009
▴
20
That is a great comparison! :) It definitely looks that way. :)
It's not about taxonomy, but about reconstructing metabolic pathways direc…
Comment: How to connect the UCSC when i get the DMR.plot?
by
Wren
•
0
I tried using the main site but it still didn't work. Thanks anyway, I'll try other methods.
Answer: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
Mensur Dlakic
★
29k
If you want an overall taxonomic profile, this tool will do it from reads directly:
https://github.com/DessimozLab/read2tree
> Well, …
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
by
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
▴
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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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…
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