Biostar Systems

Comment: STAR vs Novoalign IGV Browser visualization
by
chasem

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10

That is good to know that it isn’t just my set of reads…still concerning, though.

Comment: STAR vs Novoalign IGV Browser visualization
by
chasem

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10

I was not expecting this — not sure what to make of it yet.

That said, I did end up reading the STAR documentation more closely. This tim…

Comment: GSE28955 – Agilent-016436 Human miRNA Microarray 1.0
by
Gordon Smyth

★

3.0k

Thanks for the tutorial Kevin. A minor comment, one never needs to do this `expr <- project.bgcorrect.norm.filt.mean$E`. Just pass the whol…

Comment: How to create a label variable from a binary matrix with multiple columns
by
biogamer.31

0

I have no a table but I know which code belong to specific bacterial species. In the example, the next codes belong to specific label:

Comment: getting paired end datasets from SRA
by
Kevin Blighe

76k

‘99% of the time’, this works ‘all the time’:

fastq-dump –split-files SRR13310323

It will download anything there on the record. I t…

Answer: Basic logic and use of PERMANOVA for microbiome data
by
matteolifilipe

&utrif;

10

A bit late but might help anyone.
We use PERMANOVA to compare centroids of groups of samples, usually represented through PCoA or NMDS. Th…

Comment: MiRBase miRNA analysis with STAR
by
GenoMax

105k

How about using a [dedicated workflow][1] that is meant to this type of analysis. STAR is not the best tool for aligning small RNA’s with a…

Answer: How to extract ancestral sequence for Cow from 46 eutherian mammals EPO Ensembl?
by
minesrebollo

0

Hi Claire, I had to do the same thing with rice’s EPO. Rice was also the reference species for the alignment. By plotting some trees with i…

Answer: how to split paired-end fastq by barcode from smart-seq2
by
Divon

&utrif;

10

You can use my Genozip tool:

“`
genozip myfile.fq.gz –fast
genocat –grep-w TTAGGC myfile.fq.genozip # output all reads with the barcod…

Comment: How to create a label variable from a binary matrix with multiple columns
by
rpolicastro

5.5k

How do you know that `X543.7` is `C` for example? Do you have some sort of table that has this information?

Comment: Retrieving phytozome data using the R bioconductor package biomaRt
by
Mike Smith

&starf;

1.7k

Yes, you should start a new thread on the Bioconductor support site with the code that generates the error and the output of `sessionInfo()`

Comment: How to create a label variable from a binary matrix with multiple columns
by
biogamer.31

0

Thank you Ram. I have already updated the question. Please, I will be very grateful by your awesome help.

Comment: Where should a biologist start when learning computational biology & systems bio
by
jared.andrews07

&starf;

11k

> In general Windows WSL is almost on par with Linux – the usability problems come from not being able to execute programs with graphics ba…

Comment: normalization to “housekeeping” genes of RNAseq data vs qPCR result
by
ATpoint

52k

> Do you think we should normalize to total cell number in bulk RNAseq?

No, I do not see how this a) would be possible and b) would make s…

Comment: normalization to “housekeeping” genes of RNAseq data vs qPCR result
by
cwwong13

0

I totally agree with you on doing the qPCR validation thing, but sadly, it seems still a common practice among experimental biologists.

I…

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