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User: A. Domingues

gravatar for A. Domingues
A. Domingues • 2.4k
Reputation:
2,400
Status:
Trusted
Location:
Dresden, Germany
Website:
http://adomingues.gith...
Twitter:
keyboardpipette
Last seen:
3 hours ago
Joined:
8 years, 4 months ago
Email:
a***********@gmail.com

I analyse -omics data and try to make sense of it. I used to work at the bench, but it has been long enough that I can consider myself a bioinformatician now.

Posts by A. Domingues

<prev • 263 results • page 1 of 27 • next >
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Comment: C: Reads mapped on wrong strand
... No problem (you can click the accept bottom if you are happy with the answer). One more note, if you are going to count reads mapping to genes with something like `featureCounts` or `HTseq-count`, those tools will have have a library flag to be set to the library protocol - to count the reads correc ...
written 12 days ago by A. Domingues • 2.4k
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Comment: C: Reads mapped on wrong strand
... I was not aware of that, good to know. I normally use one of STAR/bowtie/bwa, and AFAIK, there is no option to correct on those (I am happy if someone tells me I am wrong). For pseudo-alignment, `salmon` will autodetect the library protocol. ...
written 12 days ago by A. Domingues • 2.4k
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Comment: C: Reads mapped on wrong strand
... In the reverse strand library prep (also know as dUTP based) what gets sequenced is not the original RNA but the reverse-complement. Thus when it gets mapped it goes to the opposite strand. This diagram might explain better: http://onetipperday.sterding.com/2012/07/how-to-tell-which-library-type-to- ...
written 13 days ago by A. Domingues • 2.4k
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Answer: C: Reads mapped on wrong strand
... Depending on the library preparation method (dUTP based), this could be completely normal. ...
written 13 days ago by A. Domingues • 2.4k
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Comment: C: Integrate single-cell datasets (TPM and raw) to find gene markers between cluste
... Just to add another note after doing some more research, Seurat doesn't recommend using `SCTransform` values for differential expression. So the sctransform is not even necessary for this. ...
written 13 days ago by A. Domingues • 2.4k
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Comment: C: Integrate single-cell datasets (TPM and raw) to find gene markers between cluste
... Cheers @ATpoint. This is what I feared. Cheers. I will have to go back to the drawing board. ...
written 13 days ago by A. Domingues • 2.4k
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Comment: C: Calculate strand ratio for repeat (ALU) elements
... If no one adds a valid answer in the coming days I will accept my own answer. ...
written 13 days ago by A. Domingues • 2.4k
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Answer: A: Calculate strand ratio for repeat (ALU) elements
... I shared this question on [twitter][1] and it seems that this approach appears to be ok. A few suggestions as alternative/ complementary approaches : - use repBase (or consensus) sequences instead of repeatmasker - map to genome and intersect with annotated TE coordinates. [1]: https://twitter.c ...
written 13 days ago by A. Domingues • 2.4k
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Integrate single-cell datasets (TPM and raw) to find gene markers between clusters
... Hi all, I am trying to find cell markers to distinguish population A and B using single-cell RNA-seq data publicly available. The snag is that these populations where identified in different studies, and the data is available as **raw counts** (10x) for one study and **TPMs** (Smart-seq*) for anot ...
single-cell sc seurat written 13 days ago by A. Domingues • 2.4k • updated 8 days ago by Biostar ♦♦ 20
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Comment: C: piRNA cluster annotation of non-model organisms
... I am glad it helped :) ...
written 19 days ago by A. Domingues • 2.4k

Latest awards to A. Domingues

Scholar 12 days ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Scholar 20 days ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Scholar 6 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Epic Question 6 months ago, created a question with more than 10,000 views. For Heatmap Of Read Coverage Around Tsss
Scholar 8 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Student 8 months ago, asked a question with at least 3 up-votes. For Issue with naming convention in bedtools
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Popular Question 15 months ago, created a question with more than 1,000 views. For Project organization: make code public and keep notes private
Popular Question 17 months ago, created a question with more than 1,000 views. For Project organization: make code public and keep notes private
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Appreciated 19 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Scholar 23 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Appreciated 24 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Scholar 2.0 years ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
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