User: brunobsouzaa
brunobsouzaa • 400
- Reputation:
- 400
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- Location:
- Brazil
- Last seen:
- 1 day, 3 hours ago
- Joined:
- 5 years, 5 months ago
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Posts by brunobsouzaa
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Comment:
C: Is trimming necessary for RNAseq?
... I don't perform trimming at all but I do apply some filters for genes with really low read counts. Also, a results validation helps a lot! But, you can perform some tests and compare results with trimmed and not trimmed data, this will give you a really good direction on what to do! ...
written 6 days ago by
brunobsouzaa • 400
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... I work with targeted sequencing and I like to use `cnvkit` and `ExomeDepth` for CNV calls. Take a look into their respective manuals, might help you!
`convading` is also a good tool, but it's too slow! ...
written 6 days ago by
brunobsouzaa • 400
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Comment:
C: does RSEM need STAR?
... See [here][1]
[1]: https://github.com/bli25broad/RSEM_tutorial ...
written 8 days ago by
brunobsouzaa • 400
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... Actually not. Take a look at gnomAD FAQ. The number of samples in Exome and Genome studies is very different! ...
written 14 days ago by
brunobsouzaa • 400
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... Perhaps you're looking at genome and exome AF! ...
written 14 days ago by
brunobsouzaa • 400
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Answer:
C: Convert CSV to PED
... Taken from [here][1]
If your .csv file contains data reqired for .ped and .map formats you can use it directly. For the .ped mandatory columns are: Family ID, Individual ID, Paternal ID, Maternal ID, Sex (1=male; 2=female; other=unknown), Phenotype. You need these data to run Plink. Then instead of ...
written 19 days ago by
brunobsouzaa • 400
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... If you use different genome versions yes, it will give you wrong annotations! ...
written 28 days ago by
brunobsouzaa • 400
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... Just to check if I understood, you have SNP data with hg19 coordinates and you want to annotate with hg38 coordinates? Don't do this, use the same genome version to annotate your files. ...
written 28 days ago by
brunobsouzaa • 400
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Comment:
C: problem with a for loop
... Oh, now I got it! You can simply remove the intermediate files as soon as they are used (I do this!) or you can try to use pipe `|` between your functions. I've never tried this approach but doesn't hurt to try! ...
written 5 weeks ago by
brunobsouzaa • 400
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Comment:
C: problem with a for loop
... Can you try this? `OUTPUT=/dev/stdout/$i.bam` on your first command and check the output?
...
written 5 weeks ago by
brunobsouzaa • 400
Latest awards to brunobsouzaa
Centurion
14 days ago,
created 100 posts.
Popular Question
19 days ago,
created a question with more than 1,000 views.
For Trying to visualize .bed file
Supporter
6 weeks ago,
voted at least 25 times.
Scholar
8 weeks ago,
created an answer that has been accepted.
For A: Bash script for calling CNVs using cnvkit
Teacher
8 weeks ago,
created an answer with at least 3 up-votes.
For A: How to analyze Illumina RNASeq data
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: How to analyze Illumina RNASeq data
Scholar
16 months ago,
created an answer that has been accepted.
For A: Bash script for calling CNVs using cnvkit
Popular Question
4.3 years ago,
created a question with more than 1,000 views.
For Trying to visualize .bed file
Popular Question
4.3 years ago,
created a question with more than 1,000 views.
For Doubt on filtering data from .VCF file
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