User: biofalconch

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biofalconch410
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Mexico
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5 years, 3 months ago
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Posts by biofalconch

<prev • 86 results • page 1 of 9 • next >
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Answer: A: Use PWM from CISBP-rna to find motif with MEME (FIMO)
... Maybe a little bit late but here is a workaround I did. You have to transpose the matrix so that it looks like this: GeneID A: 0.5 0.5 0 C: 0 0 0.5 G: 0.5 0 0 T: 0 0.5 0.5 I'm not going to post the script since it is a little convoluted but the only thing is ...
written 25 days ago by biofalconch410
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Comment: C: topGo analysis with PANTHER.db
... Have a look at section 4.3 of the manual, it might help ...
written 4 weeks ago by biofalconch410
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Comment: C: genome length and kmer size
... Hmmm this sounds like homework question rather than a real problem lol. But I think kmer's have 0 chance of repeating if the kmer size is equal to the genome size ...
written 4 weeks ago by biofalconch410
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Comment: C: parent GO terms
... I'd recommend looking at [this thread][1] ;) [1]: https://www.biostars.org/p/294268/ ...
written 4 weeks ago by biofalconch410
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Comment: C: Transcriptome Assembly with rnaSPAdes
... I went through the changelogs and they seem to have improved the assembler, specially by implementing a multi kmer assembly. However, I do not know if this has a real impact on the assembly, might be worth to take a look. ...
written 3 months ago by biofalconch410
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Comment: C: PSI-BLAST out put is empty
... I think shell its confusing the environmental variable, so instead of searching for $Pxxx it is looking for a variable called $Pxxx.pssm for example. To fix this, maybe try using brackets like this ${Pxxx}.pssm. Good Luck! ...
written 3 months ago by biofalconch410
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Comment: C: Detection of duplicated regions in RNA-seq data
... It is a little bit confusing that you use genome terms trying to explain RNA-seq, but here is my take on it. Basically I think this could be solve doing a differential gene expression analysis, to see if expression of gene A is greater in condition X over condition Y. Then if you are looking for a s ...
written 3 months ago by biofalconch410
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Comment: C: Specific question about the strands in Illumina paired-end libraries
... Hi Diego, > Is it possible to generate a pair of reads in the opposite direction? (as in Fragment B). If possible, why is that so? Is it because of the sequencing adapters? Yes, it is totally because of the sequencing adapters, remember that they are not specific so they will bind to either str ...
written 3 months ago by biofalconch410
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Quantifying overlapping RNA-seq paired-end reads
... Hi all, I'm working with some sequencing data, and I have noticed that all of my reads overlap with their mate, so I get a concordant alignment, however they are represented as two lines in the sam alignment. But my question is: is it ok if I use the bam file with the two lines of the alignment to ...
rna-seq written 17 months ago by biofalconch410 • updated 16 months ago by liruiradiant10
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Comment: C: Determine GO hierarchy in a list of GO terms
... Yeap: https://bioconductor.org/packages/release/data/annotation/html/GO.db.html ...
written 22 months ago by biofalconch410

Latest awards to biofalconch

Teacher 16 days ago, created an answer with at least 3 up-votes. For A: PBS script on cluster
Popular Question 13 months ago, created a question with more than 1,000 views. For RNA-seq Differential Expression Analysis
Popular Question 15 months ago, created a question with more than 1,000 views. For RNA-seq Differential Expression Analysis
Popular Question 15 months ago, created a question with more than 1,000 views. For small non-coding RNA
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: PBS script on cluster
Popular Question 16 months ago, created a question with more than 1,000 views. For RNA-seq Differential Expression Analysis
Popular Question 17 months ago, created a question with more than 1,000 views. For RNA-seq Differential Expression Analysis
Popular Question 18 months ago, created a question with more than 1,000 views. For RNA-seq Differential Expression Analysis
Popular Question 23 months ago, created a question with more than 1,000 views. For miRNA aligment with miRBase parameters
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Popular Question 2.0 years ago, created a question with more than 1,000 views. For miRNA aligment with miRBase parameters
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: plant housekeeping genes without paralogs
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