User: fatimarasool135

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Posts by fatimarasool135

<prev • 110 results • page 3 of 11 • next >
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Comment: C: how to set Deseq factor
... I have six RNAseq sample. ...how can i set the replicates ? Mean I havee to take the RNA from sample and sequenced it .? ...
written 11 months ago by fatimarasool13560
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how to set Deseq factor
... Hi , I am new to R and this tool. i am following this given script [https://gist.github.com/stephenturner/f60c1934405c127f09a6][1] I want to do differential gene expression in my six samples. I want compare the expression of six samples .i have no control and exp data sample. i have simply six ...
software error R next-gen rna-seq assembly written 11 months ago by fatimarasool13560
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Comment: C: count matrices for genes and transcripts for all samples
... Hi Haci, I have use this method. which is written in manual of stringtie. I did not use the i option with list of samples because in this method i got error of incorrect path so i use the other method. that is list below...I have run this command for 3 samples . now i have 6 files fo ...
written 11 months ago by fatimarasool13560
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Comment: C: count matrices for genes and transcripts for all samples
... Hi AT point, I have run this command for all samples python prepDE.py ./ballgown/sample1/sample1.gtf python prepDE.py ./ballgown/sample2/sample2.gtf python prepDE.py ./ballgown/sample3/sample3.gtf Two output files are generated in each run. Then i renamed files according to sample in command. a ...
written 11 months ago by fatimarasool13560
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count matrices for genes and transcripts for all samples
... Hi According to this protocol http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual I have generated the gtf files for ballgown but now i want to use the Deseq. for the Deseq tool i have to generate the text file of gene and transcripts files. I have run the python script for one samples a ...
software error assembly alignment rna-seq written 11 months ago by fatimarasool13560 • updated 11 months ago by Haci370
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htseq-count error while bam file was sorted by name
... Hi. I have encountered error while working on htseq-count. I have studied this error on many form. The solution to this error was sort the bam file by name. I did same by using this command as samtools sort -n myfile_align.bam -o myfile_sortedn.bam then i run the comand on htseq as h ...
software error assembly alignment rna-seq R written 11 months ago by fatimarasool13560
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Comment: C: gene sequence fetching from bam or fastq file of rna seq data
... Hi buffo , this command grep -A 1 'gene_id' transcript.fa display only one line of sequence , i want to extract the full length of gene sequence ...
written 11 months ago by fatimarasool13560
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Comment: C: gene sequence fetching from bam or fastq file of rna seq data
... Hi buffo , please reply me ...
written 11 months ago by fatimarasool13560
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Comment: C: gene sequence fetching from bam or fastq file of rna seq data
... Hi buffo, I have genrated the sequence file (transcript.fa). this file contain sequence ids like STRG.14.145 gene =STRG.14 Here i have write the id of first sequence in file. My gene of interest id is TraesCS3D02G273600. I want to do extract this id sequence from the file i have generat ...
written 11 months ago by fatimarasool13560
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graphs plotong by ballgown
... I want to plot several samples at once I have run this command plotTranscripts('TraesCS1B02G048400', bg_chrX, samples=c('G1', 'G2', 'G3', 'G4'),meas='FPKM', colorby='transcript') The error got is > Error in seq.default(min(gtrans$start), max(gtrans$end), by = 1) : > 'from' must be a f ...
software error R rna-seq written 12 months ago by fatimarasool13560

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