User: newbie

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newbie90
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Posts by newbie

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Comment: C: How to get transcript ID and tpm from the gtf files of ballgown outputs?
... 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 newbie90
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How to get transcript ID and tpm from the gtf files of ballgown outputs?
... 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 / ...
gtf ballgown hisat2 rna-seq awk written 5 weeks ago by newbie90 • updated 5 weeks ago by _r_am32k
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Comment: C: Kmeans in R for clustering on significant gene list by sample
... 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 newbie90
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Problem with bedtools intersect with two gtfs
... 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 ...
gtf bedtools intersect rna-seq written 8 weeks ago by newbie90
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Comment: C: Is it good to merge transcripts tpm to gene which is of different gene type?
... 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 newbie90
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Is it good to merge transcripts tpm to gene which is of different gene type?
... 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 ...
tpm kallisto rna-seq written 10 weeks ago by newbie90 • updated 10 weeks ago by wensulin930
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Comment: C: Why counts to tpm gives different values compared to tpm from kallisto?
... 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 newbie90
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Comment: C: Why counts to tpm gives different values compared to tpm from kallisto?
... 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 newbie90
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Why counts to tpm gives different values compared to tpm from kallisto?
... 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 ...
featurecounts tpm kallisto rna-seq rawcounts written 11 weeks ago by newbie90
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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 newbie90

Latest awards to newbie

Centurion 3 months ago, created 100 posts.
Popular Question 4 months ago, created a question with more than 1,000 views. For How to get read counts on transcript level using featurecounts?
Popular Question 5 months ago, created a question with more than 1,000 views. For Differential analysis show different results with edgeR and in box plot with t-test
Supporter 8 months ago, voted at least 25 times.
Popular Question 9 months ago, created a question with more than 1,000 views. For How to filter low expressed genes based on TPM expression?

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