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User: Pin.Bioinf

gravatar for Pin.Bioinf
Pin.Bioinf • 170
Reputation:
170
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Trusted
Location:
Malaga
Last seen:
3 days, 15 hours ago
Joined:
1 year, 6 months ago
Email:
i*************@gmail.com

Im a Health Engineer with a Bioinformatics specialization doing epigenetics research.

Posts by Pin.Bioinf

<prev • 100 results • page 1 of 10 • next >
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Comment: A: Total RNA-Seq vs mRNA-Seq
... I do not understand a lot about biology as I am a computer scientist. My colleague asked me if she could add more samples to the run (which would diminish the amount of reads per sample), so I am asking the minimum amount of M reads needed in both cases: total rnaseq and mrnaseq. So what I underst ...
written 11 days ago by Pin.Bioinf • 170
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Comment: C: Total RNA-Seq vs mRNA-Seq
... Thank you WouterDeCoster, so you mean if I do not deplete rrna I should need 600 -1000 M reads per sample? And what if I do ribosomal depletion first? ...
written 11 days ago by Pin.Bioinf • 170
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Total RNA-Seq vs mRNA-Seq
... Hello, I have read that 30-50M reads mapped per sample are the general optimal number of reads mapped needed to do a DE expression analysis for mRNA-Seq. What would be the minimum for TOTAL RNA-Seq? Is it a lot more? Thank you ...
rna-seq written 11 days ago by Pin.Bioinf • 170 • updated 10 days ago by kristoffer.vittingseerup • 810
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Comment: C: Tool for computing Tumor Mutational Burden?
... Yes, I posted a question asking if this was possible on RNA-Seq, this question is not about RNA-Seq but in general. Nobody told me what tools can be used to do it, and there are no posts on how this can be done (tools, pipelines...). ...
written 18 days ago by Pin.Bioinf • 170
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(Closed) Tool for computing Tumor Mutational Burden?
... Hello, I know that Tumor Mutational Burden is the 'number of variants per megabase' but, how can I compute this? are there any bcftools or samtools commands or R packages that can obtain this information from the vcf files? I have no idea about this, sorry. Thank you ! ...
tmb mutation written 18 days ago by Pin.Bioinf • 170
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Comment: C: Can I compute Tumour Mutational Burden from rnaseq fastq files?
... Thanks a lot! Actually I saw that post but did not know mutational load was similar to mutational burden. Thanks ...
written 21 days ago by Pin.Bioinf • 170
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Can I compute Tumour Mutational Burden from rnaseq fastq files?
... Hello, I am not familiar with tumour mutational burden, but I was asked to obtain it from fastq files sequenced with RNA-Seq. How can I do it with this data? I think it would be better with exome sequencing though. Thank you ...
vcf tmb rna-seq snp written 21 days ago by Pin.Bioinf • 170
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(Closed) Can I get the SNPs from my RNA-Seq fastq files?
... Hello, I was asked if I can know/obtain the SNPs in the samples we sequenced with RNA-Seq. Can I do it from the .fastq files? How can I do it? Also, these fastq files mapped agains reference with 50M reads, would that be enough? Do I need to compute coverage? Thank you ...
fastq rna snp rna-seq written 23 days ago by Pin.Bioinf • 170 • updated 23 days ago by S AR • 50
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Comment: C: Sequenced sample twice, can I merge the fastqs to analyze?
... Okay, thank you. Maybe so my colleague agrees that it is not a good idea I could check if the replicates are consistent plotting a PCA (and probably this will show they are not similar) so then I can convince her it is not a good idea? ...
written 4 weeks ago by Pin.Bioinf • 170
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Sequenced sample twice, can I merge the fastqs to analyze?
... Hello, my colleague sequenced (RNA-Seq) some samples a month ago and the quality of some of them was not so good. She sequenced some new samples and also some of the bad quality samples again to analyze them again. She is asking me if, in order to have more reads and better results, I can re-use th ...
rnaseq fastq written 4 weeks ago by Pin.Bioinf • 170 • updated 4 weeks ago by geek_y ♦ 8.8k

Latest awards to Pin.Bioinf

Centurion 11 days ago, created 100 posts.
Supporter 9 weeks ago, voted at least 25 times.
Scholar 9 weeks ago, created an answer that has been accepted. For A: STAR --quantMode GeneCounts function
Autobiographer 18 months ago, has more than 80 characters in the information field of the user's profile.
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