User: chahat_u

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chahat_u110
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Posts by chahat_u

<prev • 71 results • page 1 of 8 • next >
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Comment: C: How do you find novel transcripts using GFFcompare?
... Hi Wouter, thanks for letting me know. I tried to search on that other site if cross-posting is OK, and the sense that I got was that [its not necessarily a bad thing][1], although I do understand your point of people spending double the amount of time. Therefore I waited for 3 days and when there w ...
written 4 days ago by chahat_u110
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How do you find novel transcripts using GFFcompare?
... Hi, I am trying to find novel transcripts from an RNA-seq database ([as mentioned in my previous question][1]). Based on the advice I got, it seemed that using Stringtie for transcript assembly is a good way to go, and it supports novel transcript discovery even with the reference GTF file provided ...
rna-seq gffcompare written 10 days ago by chahat_u110
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Comment: C: Where to find a valid GTF file for stringtie asssembly?
... hey, did you find the GTF file you were looking for? I am also looking for it ...
written 12 days ago by chahat_u110
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Comment: C: Can you detect novel (non-coding) transcripts using Salmon and the hg38 transcri
... Hi Lieven, thank you for your response. You mention option 1 as the way to go, but in another answer to this question, Kristoffer says that he doesn't see a point in using Trinity for human samples as its highly likely to find any new transcripts in human samples. You also mention something similar ...
written 18 days ago by chahat_u110
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Comment: C: Can you detect novel (non-coding) transcripts using Salmon and the hg38 transcri
... Hi Kristoffer, thank you for your response. The linked bioconductor page is also very helpful! I had a question about what you said. Here you mention that for de-novo transcript reconstruction, Cufflinks/StringTie are good options. Whereas in the linked page you mention Salmon/Kallisto being good op ...
written 18 days ago by chahat_u110
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Comment: C: Can you detect novel (non-coding) transcripts using Salmon and the hg38 transcri
... Hi Wouter, thank you for the answer. I meant novel transcripts that could be lncRNA/eRNA because they overlap with available DNAse Hypersensitivity data. In other words, the DHS data tells us that all these regions in the DNA are open access, and then we see that actually they produce transcripts to ...
written 20 days ago by chahat_u110
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Can you detect novel (non-coding) transcripts using Salmon and the hg38 transcriptome?
... Hi, This might be another naive question. I have RNA-Seq data from 2 different types of samples (pain vs no-pain), and I want to **identify novel lncRNA/eRNA in pain**. I also have DHS/ATAC data for that gives me accessible regions in the DNA, some of which would be regulatory. One way to do thi ...
rna-seq written 20 days ago by chahat_u110
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Comment: C: Measure expression level of a single (novel) transcript in multiple fastq files
... Thanks Lieven, that was quite helpful! Also, is there any advantage to using this approach to quantify the differential expression of this novel transcript, as compared to using genome-guided methods like Cufflinks etc? Especially given that this is in human ...
written 4 weeks ago by chahat_u110
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Measure expression level of a single (novel) transcript in multiple fastq files
... Hi, This maybe a silly question, but I want to quantify the expression level of a specific transcript across many single-end fastq files. The transcript in question is a novel one, and I don't think its in the HG38 transcriptome. Using `salmon` gives me the abundance of ALL transcripts in ONE fastq ...
rna-seq written 4 weeks ago by chahat_u110
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Comment: C: How to find read count for a newly discovered transcript
... Thanks Lieven. I have a couple of questions about that. First, regarding mapping the transcript to the genome, wouldn't only the exonic regions be mapped, since the transcript may not have the intronic region? Secondly, I never knew about mapping reads to a transcriptome. Is there a popular software ...
written 3 months ago by chahat_u110

Latest awards to chahat_u

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Popular Question 3 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Popular Question 5 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Voter 5 months ago, voted more than 100 times.
Popular Question 10 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Popular Question 10 months ago, created a question with more than 1,000 views. For Doing GSEA analysis on a set of genes
Popular Question 10 months ago, created a question with more than 1,000 views. For Extracting 5'UTR and 3'UTR bed files from gtf file
Student 10 months ago, asked a question with at least 3 up-votes. For Low mapped percentage. How to know if data is junk?
Student 20 months ago, asked a question with at least 3 up-votes. For Low mapped percentage. How to know if data is junk?
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