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Search: Posts Made By: Dario1984
Forum: Bioinformatics 07-06-2018, 12:00 AM
Replies: 1
Views: 599
Posted By Dario1984
No; tumour and normal samples are not unwanted...

No; tumour and normal samples are not unwanted technical variation. They are phenotypes of biological interest. A lot of analyses have been done with TCGA data and published, so I think you could...
Forum: RNA Sequencing 07-05-2018, 10:59 PM
Replies: 1
Views: 776
Posted By Dario1984
You can't simply use GSEA on short read RNA-seq...

You can't simply use GSEA on short read RNA-seq data counts. The number of alignments counted for a gene is proportional to its abundance and its length. You need to normalise for gene length.
Forum: Bioinformatics 02-07-2018, 10:29 PM
Replies: 4
Views: 829
Posted By Dario1984
If the new version of the genome is of higher...

If the new version of the genome is of higher quality and more complete, you would have lost all of those reads which did not map to the previously used genome but could map to the new genome,...
Forum: Bioinformatics 11-12-2017, 10:00 PM
Replies: 5
Views: 1,099
Posted By Dario1984
RNA-seq differential expression methods are known...

RNA-seq differential expression methods are known to be affected by outliers. You have used edgeR to analyse the dataset. What dispersion estimation variety did you use? If you have patient...
Forum: Bioinformatics 06-27-2017, 11:00 PM
Replies: 6
Views: 782
Posted By Dario1984
It's always best to do adapter trimming, even if...

It's always best to do adapter trimming, even if the aligner you use later can do soft-clipping, such as STAR. It would work moderately faster if it didn't have to attempt to map the adapter...
Forum: Bioinformatics 05-02-2017, 06:00 PM
Replies: 20
Views: 12,342
Posted By Dario1984
That is not a random chromosome, but an...

That is not a random chromosome, but an alternative version of part of a chromosome that has lots of variability in the human population. It means that the person you sequenced now has a reference...
Forum: Bioinformatics 04-30-2017, 06:00 PM
Replies: 20
Views: 12,342
Posted By Dario1984
What do you mean by random chromosome? The...

What do you mean by random chromosome? The reference assembly doesn't contain random sequences.
Forum: RNA Sequencing 04-27-2017, 01:00 AM
Replies: 6
Views: 2,778
Posted By Dario1984
It depends on what TPM is an abbreviation for. It...

It depends on what TPM is an abbreviation for. It sometimes means Tags Per Million and other times means Transcripts Per Million. I was thinking about Tags Per Million but the question asked was...
Forum: RNA Sequencing 04-26-2017, 06:00 PM
Replies: 6
Views: 2,778
Posted By Dario1984
I would use the FPKM you obtained from Cufflinks....

I would use the FPKM you obtained from Cufflinks. Before you do, check the range of FPKM values calculated by Cufflinks. We find some are theoretically impossible values by considering how many reads...
Forum: Bioinformatics 04-25-2017, 08:00 PM
Replies: 20
Views: 12,342
Posted By Dario1984
I agree that there are a lot of publicly...

I agree that there are a lot of publicly available exome sequencing datasets that use hg19. I recommend using the results based on hg38 and converting them into some gene-based naming format, such as...
Forum: Illumina/Solexa 04-25-2017, 07:00 PM
Replies: 4
Views: 991
Posted By Dario1984
We use Trinity (http://trinityrnaseq.github.io)...

We use Trinity (http://trinityrnaseq.github.io) because we found its results can be experimentally validated by biologists. There's also a genome guided assembly mode...
Forum: RNA Sequencing 04-24-2017, 11:00 PM
Replies: 6
Views: 2,778
Posted By Dario1984
Of course it makes a substantial difference. TPM...

Of course it makes a substantial difference. TPM doesn't normalise by the length of the gene, FPKM does. Are you comparing between genes, such as by plotting the gene expression values in a heatmap?...
Forum: Bioinformatics 04-24-2017, 10:00 PM
Replies: 5
Views: 1,938
Posted By Dario1984
I contacted QIAGEN support last year about this...

I contacted QIAGEN support last year about this topic. CLC Genomics Workbench has no specific algorithm for assembling RNA-seq data. The support officer explained:



Also, CLC Genomics Workbench...
Forum: Illumina/Solexa 04-24-2017, 08:00 PM
Replies: 4
Views: 991
Posted By Dario1984
I have noticed similar problems with Cufflinks in...

I have noticed similar problems with Cufflinks in the past. Our research group no longer uses it because it hasn't been updated in 3 years and some of the FPKM values look suspicious, which you have...
Forum: Bioinformatics 04-24-2017, 07:00 PM
Replies: 20
Views: 12,342
Posted By Dario1984
hg38 is a corrected and improved version of hg19....

hg38 is a corrected and improved version of hg19. You should use the newer and better assembly. You should also specify which version of hg38 you use. The latest version...
Forum: Academic/Non-Profit Jobs 04-24-2017, 06:00 PM
Replies: 7
Views: 1,713
Posted By Dario1984
It's probably a fixed-term contract, which is...

It's probably a fixed-term contract, which is something for potential applicants to consider if they're applying for a home loan and need more certainty regarding employment. Also, having an...
Forum: Illumina/Solexa 02-16-2017, 06:00 PM
Replies: 8
Views: 1,687
Posted By Dario1984
When will the 1919 novel alleles be added to the...

When will the 1919 novel alleles be added to the IMGT/HLA database?
Forum: Bioinformatics 12-21-2016, 07:00 PM
Replies: 4
Views: 2,297
Posted By Dario1984
STAR doesn't do adapter trimming, but it does do...

STAR doesn't do adapter trimming, but it does do soft-clipping, which gives the same effect. I also have a dataset where the pairs of reads largely overlap, so I also need to merge the pairs into a...
Forum: Bioinformatics 12-15-2016, 11:00 PM
Replies: 7
Views: 17,890
Posted By Dario1984
Scaled estimate and normalised count are similar...

Scaled estimate and normalised count are similar ways of normalising the reads of each sample. Neither one is better and both are fine. Make a scatterplot of scaled estimate vs. normalised count to...
Forum: Bioinformatics 12-13-2016, 11:02 PM
Replies: 1
Views: 862
Posted By Dario1984
You can use bowtie2-build to build an index for...

You can use bowtie2-build to build an index for mapping with bowtie2.
Forum: RNA Sequencing 12-13-2016, 10:05 PM
Replies: 4
Views: 2,392
Posted By Dario1984
The U6 promoter sequence is not a fixed number of...

The U6 promoter sequence is not a fixed number of bases from the 5' end. In my dataset, I see the start of the promoter frequently between positions 10 and 18.

A better method is to find the start...
Forum: Bioinformatics 11-29-2016, 10:00 PM
Replies: 213
Views: 60,339
Posted By Dario1984
But can it output chimerically mapped reads to a...

But can it output chimerically mapped reads to a separate output file, like STAR can? There's no mention of chimeric reads in the user guide, so I'm not sure if it's even suitable for that case.
Forum: Bioinformatics 11-02-2016, 04:00 PM
Replies: 3
Views: 1,038
Posted By Dario1984
Trimming is the best way to make the datasets...

Trimming is the best way to make the datasets comparable.
Forum: Bioinformatics 11-02-2016, 12:00 AM
Replies: 2
Views: 1,045
Posted By Dario1984
You have two groups of genes and every gene has a...

You have two groups of genes and every gene has a different length to every other gene. Longer with the same rate of transcription of shorter genes will have more counts. Also, different genes have...
Forum: General 10-18-2016, 12:00 AM
Replies: 1
Views: 1,529
Posted By Dario1984
That simply means that SummarizedExperiment had...

That simply means that SummarizedExperiment had its definition changed recently and your variable doesn't have the new slot because it was created before the new definition was in existence. You can...
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