User: HK

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HK20
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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 10 days 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 10 days 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 10 days 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 10 days ago by HK20 • updated 10 days ago by Nicolas Rosewick5.5k
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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 11 days 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 12 days 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 12 days 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 12 days ago by HK20 • updated 12 days ago by Devon Ryan71k
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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 12 weeks 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 8 months ago by HK20

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