User: Martombo

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Martombo1.8k
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Seville, ES
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Posts by Martombo

<prev • 219 results • page 1 of 22 • next >
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Comment: C: topGO is performing enrichment test on GO terms that are not present in my datas
... I could reproduce your error, but I don't know what causes it. Are these unexpected GO terms connected to the ones actually associated to your gene? Maybe their significance could come from the GO network structure, but that would be strange. It looks like a bug to me, you should definitely ask abou ...
written 6 hours ago by Martombo1.8k
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Comment: C: Why does cufflinks split this transcript?
... I'm sorry I don't have any other ideas as I'm not an expert. For transcript quantification cufflinks has long been known for being sub-optimal, maybe some other software that is specifically built for assembly like SPAdes or Trinity would be a better choice? ...
written 21 hours ago by Martombo1.8k
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Comment: C: Why does cufflinks split this transcript?
... did you check how do they overlap the junction? maybe a majority of them only has few bases on one exon... ...
written 1 day ago by Martombo1.8k
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Comment: C: Why does cufflinks split this transcript?
... that's the junction with the most reads in the whole transcript do you know if these reads are uniquely mapped? ...
written 4 days ago by Martombo1.8k
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Comment: C: RNA seq- without a control
... I think OP mentioned that he can indeed distinguish between host and pathogen transcriptome and that the focus is on the latter. ...
written 28 days ago by Martombo1.8k
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Comment: C: RNA seq- without a control
... It makes perfect sense to compare the two conditions in deseq2 / edger. There is no strict necessity of having control - treatment pairs. The question this comparison would answer is about the transcriptional differences in the two states of the pathogens. Do you actually want to compare the host tr ...
written 28 days ago by Martombo1.8k
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Comment: C: How to get each exon counts from TCGA
... thanks, that looks like a neat repository. I can't find exon counts however, while they have isoform and gene data. ...
written 4 weeks ago by Martombo1.8k
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Answer: A: How to get each exon counts from TCGA
... For those passing by this question: at the time of speaking (end of 2017) TCGA exon counts data are not present on the harmonized [data portal][1], so if you want to get these data you'll have to scavenge through the [legacy portal][2], where different genome versions and annotations are used. You c ...
written 4 weeks ago by Martombo1.8k
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Comment: C: Why Warning: reads with missing mate encountered is occured in HTSeq?
... ah, sorry, I didn't realize 5 days had passed already ;) ...
written 6 weeks ago by Martombo1.8k
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Comment: C: Why Warning: reads with missing mate encountered is occured in HTSeq?
... Was the sorted bam file created correctly? Depending on your version of samtools, that might be an outdated syntax. You should use `samtools sort -n -T /tmp/aln.sorted -o aln.sorted.bam aln.bam`, see [here][1]. [1]: http://www.htslib.org/doc/samtools.html ...
written 6 weeks ago by Martombo1.8k

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Popular Question 25 days ago, created a question with more than 1,000 views. For different output format in Clustal-Omega
Scholar 7 weeks ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Appreciated 6 months ago, created a post with more than 5 votes. For A: Tophat --max-multihits option
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Great Question 8 months ago, created a question with more than 5,000 views. For Sjdboverhang Option In Star
Appreciated 10 months ago, created a post with more than 5 votes. For A: Tophat --max-multihits option
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Popular Question 17 months ago, created a question with more than 1,000 views. For different output format in Clustal-Omega
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Popular Question 20 months ago, created a question with more than 1,000 views. For misc_RNA in Ensembl
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 23 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Scholar 2.1 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 2.3 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: Tophat --max-multihits option
Guru 2.5 years ago, received more than 100 upvotes.
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: Tophat --max-multihits option
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Sjdboverhang Option In Star
Scholar 2.7 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Scholar 2.7 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.

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