User: fatimarasool135

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Posts by fatimarasool135

<prev • 68 results • page 1 of 7 • next >
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Comment: C: separation of number of DE genes for one sample from output file obtain from ba
... Hi, I got it .I have made the two groups each contain the 3 samples in pheno_data file. Next I want to do Gene ontology and gene enrichment analysis. For gene ontology I try it on AgriGo. but this tool not take the genes id named as TraesCS3D02G273600. how can I do gene ontology of wheat. I am ne ...
written 21 days ago by fatimarasool13520
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separation of number of DE genes for one sample from output file obtain from ballgown.
... Hi, I have use the ballgown for differential gene expression. I have the six sample in my data set. The final list of differential gene expression obtain from the ballgown contain no sample name information from which I can calculate the number of DE gene in corresponding samples. The list is as ...
gene assembly rna-seq software error written 25 days ago by fatimarasool13520 • updated 25 days ago by ATpoint17k
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Comment: C: how to interpret hisat2 result
... Hi WouterDeCoster, I can say that in my data set, Total number of reads is 5064681 in which uniquely aligned reads is 39079594 (77.16%) multi-mapped reads is 3369392 (6.65%) can you please tell me I am correct for getting information about reads in m ...
written 8 weeks ago by fatimarasool13520
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Comment: C: how to interpret hisat2 result
... Hi WouterDeCoster, Thank you. but each information is three times such as aligned concordantly exactly 1 time is three times in my summary, then how can conclude this result? What will the result/%of uniquely mapped reads? ...
written 8 weeks ago by fatimarasool13520
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Comment: A: how to interpret hisat2 result
... Hi WouterDeCoster, Thank you. but each information is three times such as ` aligned concordantly exactly 1 time` is three times in my summary, then how can conclude this result? What will the result/%of uniquely mapped reads? ...
written 8 weeks ago by fatimarasool13520
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how to interpret hisat2 result
... Hi, I have run the HISAT2 tool for alignment. The tool was run successfully but can't understand the result's summary. I want to know two information from this summary as uniquely aligned reads and multi-mapped reads. how can i get these value? The summary of my work as 50646812 reads; of thes ...
assembly alignment rna-seq written 8 weeks ago by fatimarasool13520
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The following object is masked from package:base
... Hi I have installed the ballgown package for differential gene expression. Now I called the library of the installed packages for differential gene expression. but I encountered the following errors (masked) while calling the libraries. Can you tell me how to solve these masked objects from the pa ...
software error R rna-seq written 9 weeks ago by fatimarasool13520 • updated 9 weeks ago by zx87547.5k
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ballgown stattest function error
... Hi, I have encountered an error while running the stattest function of ballgown I have run the command as > results_transcripts = stattest(bg_chrX_filt,feature= c("gene","exon","intron","transcript"),covariate="part", getFC=TRUE,meas="FPKM", timecourse = FALSE, df=2) The error was Er ...
R rna-seq written 9 weeks ago by fatimarasool13520 • updated 9 weeks ago by RamRS22k
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Comment: C: conversion of gene ids into ensembl id
... Thanks Jean elbers. Can you tell me which file contains these sequences? Because i have run the string-tie tool and ballgown.and i have not seen any file contain the sequence of genes. ...
written 9 weeks ago by fatimarasool13520
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conversion of gene ids into ensembl id
... Hi, .I did differential gene expression by using this protocol Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown I have gene list file after using the ballgown the gene id in this files is as id > MSTRG.28632 MSTRG.3615 MSTRG.7507 MSTRG.70532 MSTR ...
annotation. mapping conversion written 9 weeks ago by fatimarasool13520 • updated 9 weeks ago by jean.elbers1.1k

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Popular Question 12 months ago, created a question with more than 1,000 views. For gatk tool installation problem

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