User: newbie
newbie • 90
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... this is what I don't know how to do. Can you please help me with an example. thanq
I actually tried the below command for one of the file
grep -P "\ttranscript\t" sample.gtf | cut -f9 | awk '{gsub("\"","",$0);gsub(";","",$0);print $4,$12}'
And this gave an output like below:
MSTRG.7557 ...
written 5 weeks ago by
newbie • 90
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... I have used ballgown on 150 samples. And the ballgown outputs are like below:
Sample1
|_____ e2t.ctab
|_____ e_data.ctab
|_____ Sample1.gtf
|_____ i2t.ctab
|_____ i_data.ctab
|_____ t_data.ctab
Sample1.gtf looks:
# stringtie -e -B -p 8 -G / ...
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... Hi Kevin,
I actually have 100 interesting genes and would like to use them for classifying the samples. In this case, as I want to classify samples the matrix should have samples as rows and genes as columns. Am I right? ...
written 7 weeks ago by
newbie • 90
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... I'm trying to use bedtools intersect on `gencode annotation` gtf and another gtf which is output from `stringtie merge` option.
bedtools intersect -v -b gencode.v27.annotation.gtf -a stringtiemerge.gtf > final.gtf
This is how gencode gtf looks:
![enter image description here][1]
And this ...
written 8 weeks ago by
newbie • 90
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... My goal is to use the genes tpm for estimating immune cell infiltration. For this I have to use Gene names and their tpm. ...
written 10 weeks ago by
newbie • 90
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... I have gene expression data from kallisto with tpm expression. I would like to sum the tpm of transcripts that belong to the same gene and just summarize the `TPMs` for each gene.
But I see that same gene has a different `gene_type`. In that case can I sum the tpm of transcripts that belong to the ...
written 10 weeks ago by
newbie • 90
• updated
10 weeks ago by
wensulin93 • 0
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... I saw the effective length thing here [A review of RNA-Seq expression units][1]. Yes I feel like running kallisto now. One last question. Once I get the transcripts with tpm, can I sum the tpm of transcripts from same gene to make it gene level transcripts?
[1]: https://haroldpimentel.wordpress. ...
written 11 weeks ago by
newbie • 90
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... If you check the functions, for one of the function only `Coding_length` is used and for other function `effLength` which is calculated from `Coding_Length` is used. And yes, I did the sanity check, the results from both functions give `sum to one million`.
Among the two functions I used one is sug ...
written 11 weeks ago by
newbie • 90
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...
I have RNA-Seq data with raw counts extracted from bam files using `featureCounts`. I wanted to convert counts to tpm, because I need TPM for some analysis.
Initially, I got the coding length for each Gene like below:
library(GenomicFeatures)
gtf_txdb <- makeTxDbFromGFF("gencode.v27.a ...
written 11 weeks ago by
newbie • 90
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Comment:
C: Interpretation of two PCA plots
... Thanks for the answer. I understand that they are still similar, may I know why they are mirror images?
...
written 12 weeks ago by
newbie • 90
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