User: HK

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HK20
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3 months ago
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1 year, 7 months ago
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Posts by HK

<prev • 21 results • page 1 of 3 • next >
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Comment: C: tophat equal length problem
... well i have read that thread , but did not get any solution from that. thats why i am posting again. ...
written 3 months ago by HK20
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Comment: C: tophat equal length problem
... Well i didnt do any pre processing myself. I got the pre-processed files and have to do the mapping and stuff. Now, in such a case having different sequence and quality length for the same read what should i do, should i remove such read and how? ...
written 3 months ago by HK20
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(Closed) tophat equal length problem
... Hey, I am running an RNA seq pipeline, all my samples gave the output after mapping except one and it gives an error: prep_reads v2.1.1 (ecf7617) --------------------------- Error: qual length (76) differs from seq length (45) for fastq record ! gzip: stdout: Broken pipe Stan ...
tophat equal length fastqc written 3 months ago by HK20
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tophat equal length problem
... Hey, I am running an RNA seq pipeline, all my samples gave the output after mapping except one and it gives an error: prep_reads v2.1.1 (ecf7617) --------------------------- Error: qual length (76) differs from seq length (45) for fastq record ! gzip: stdout: Broken pipe Stan ...
tophat equal length fastqc written 3 months ago by HK20 • updated 3 months ago by Nicolas Rosewick6.0k
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Comment: C: combining quantification (featureCounts) result files into a single dataset
... Thanks @Devon. Can you please explain ths "You'll need a sampleTable, just as with the standard functions built into DESeq2." Should i just use this list.files() function and have all the .txt files saved in myfiles variable . And then pass in the function?? myfiles=list.files(pattern = "*.txt" ) ...
written 3 months ago by HK20
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Answer: A: Pathway analysis programs
... Well i have always used ingunity pathway analysis (IPA) and it recognise almost all the genes. ...
written 3 months ago by HK20
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Comment: C: combining quantification (featureCounts) result files into a single dataset
... @sej i already have the result from the featurecounts and have multiple txt files, i need to combine all the txt files in one dataframe. ...
written 3 months ago by HK20
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combining quantification (featureCounts) result files into a single dataset
... Hey All, I have almost 160 output files in a folder from the featurecounts (quantification of RNA-Seq) and now i want to put that in one datframe to be use for DESeq. The format of the fetaure counts result is havinf 7 columns: Geneid Chr Start End Strand Length Sample1 What is need is a ...
matix featurecounts combine written 3 months ago by HK20 • updated 3 months ago by Devon Ryan74k
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extracting exons and introns cordinates from the gtf file
... Hi everyone, I have a gtf file download from Gencode (##description: evidence-based annotation of the human genome (GRCh38), version 25 (Ensembl 85), ##provider: GENCODE) and now want to load this gtf in R or in linux and want to do few things 1) want to know how many exons per gene and the cordin ...
gtf exon cordinates intron cordinates written 5 months ago by HK20
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RNA Seq length distribution plot
... Hey, I am making plots for my paper, and really want to make such a plot. I want the fastq files, bam files and also the xpression (counts) file for all samples. I cant figure out how to make such a plot to show the different species that i found in my samples, show the frequency peaks as shown her ...
rna seq distribution plot written 11 months ago by HK20

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