Forum: RNA Sequencing
04-18-2019, 05:22 AM
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Replies: 0
Views: 1,919
DESeq and checkFullRank(modelMatrix)
Hello guys,
I am running DESeq2 to compare 4 different conditions and I have a problem with a commmand line.
dds = DESeqDataSetFromMatrix(countData = countMatrix, colData = coldata, design = ~...
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Forum: RNA Sequencing
04-11-2019, 08:08 AM
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Replies: 3
Views: 1,880
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Forum: RNA Sequencing
04-11-2019, 08:03 AM
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Replies: 3
Views: 1,880
Hi GenoMax,
I performed an alignment with...
Hi GenoMax,
I performed an alignment with STAR and I have serveal output files.
One output is this:
Sample1ReadsPerGene.out
The counting of the reads is already done by STAR, so why I...
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Forum: RNA Sequencing
04-11-2019, 07:18 AM
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Replies: 3
Views: 1,880
Counting and Recount reads with featureCotuns
Hello everyone,
I am using different tools for getting alignments and read count such as,
salmon and STAR.
Both of this tools have reads counted output that I could use directly into DESeq2...
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Forum: RNA Sequencing
04-09-2019, 10:38 AM
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Replies: 4
Views: 2,688
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Forum: RNA Sequencing
03-27-2019, 06:01 AM
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Replies: 4
Views: 2,688
Hi GenoMax,
unfortunately writing the...
Hi GenoMax,
unfortunately writing the entire path didn't help,
there must be something in my index structure command line that need to be adjusted I guess.
the problem is that if I want...
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Forum: RNA Sequencing
03-26-2019, 06:46 PM
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Replies: 4
Views: 2,688
STAR Aligner quantMode and fatal error
Hello Everyone,
I have problems with STAR aligner.
I want to use the quantMode option in order to have .tab file that I will use for later analysis.
The first thing I did is the index of the...
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Forum: RNA Sequencing
03-06-2019, 10:11 AM
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Replies: 0
Views: 2,079
error in DESeqDataSet
Dear all,
I have 4 RNAseq file from an experiment with two different conditions,
"Untreated" and "Treated" and after thee counting of the reads with futureCounts I'm trying to analyze it with...
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Forum: RNA Sequencing
03-05-2019, 07:59 AM
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Replies: 5
Views: 1,653
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Forum: RNA Sequencing
03-05-2019, 07:44 AM
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Replies: 5
Views: 1,653
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Forum: RNA Sequencing
03-05-2019, 06:50 AM
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Replies: 5
Views: 1,653
RNAseq from patients
Hello,
I have a question, If I have 10 Bam files (RNAseq) from 10 different patients and I want to see the different expression of few genes, what is the best tool to use after counting the reads?...
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Forum: RNA Sequencing
02-24-2019, 09:09 PM
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Replies: 2
Views: 1,553
Hi GenoMax,
What I want to do is to compare...
Hi GenoMax,
What I want to do is to compare the expression profile of cell lines of the same type of tumor. They do not have technical replicates ,they are named CUTLL1, KOPTK1, PF382, DND41.
...
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Forum: RNA Sequencing
02-24-2019, 11:15 AM
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Replies: 2
Views: 1,553
RNAseq without technical replicates
Dear all,
I want to download RNAseq files of tumor cell lines from GEO and compare between them.
I know that I can not use DESeq2 if I don't have technical replicate, so I want to ask what is the...
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Forum: RNA Sequencing
02-22-2019, 03:31 AM
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Replies: 0
Views: 1,370
DESeq2 minimum BAM files
Hello,
I have a simple question,
is there a minimum of BAM files that I have to process with DESeq2 for using it?
for example, if I have two samples, not replicates and I want to do a quick and...
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Forum: RNA Sequencing
02-21-2019, 10:24 AM
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Replies: 1
Views: 1,484
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Forum: RNA Sequencing
02-21-2019, 06:53 AM
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Replies: 1
Views: 1,484
DESeq and data frame error
Hello everyone,
I’m new to R and DESeq2 and I’m excited to get already some results.
I want to compare the gene expression of two conditions so I have 2 file.bam
I used featureCounts to...
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Forum: RNA Sequencing
02-20-2019, 05:39 AM
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Replies: 0
Views: 1,203
Transcriptome Generation -Salmon
Hello guys,
I'm analyzing the gene expression profiling in nematode and I want to generate a FASTA file containing the sequence of all the transcripts using Salmon.
It seems that the program...
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Forum: RNA Sequencing
02-19-2019, 10:15 AM
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Replies: 2
Views: 1,604
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Forum: RNA Sequencing
02-19-2019, 09:59 AM
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Replies: 2
Views: 1,604
samtools index file error
Hello,
I have to post process the outcome STAR file .bam but when I go to create an index for it I have an error with samtools,
Patrizios-MBP:star patrizio$ samtools index SRR359063.bam...
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Forum: RNA Sequencing
02-19-2019, 09:26 AM
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Replies: 6
Views: 6,921
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Forum: RNA Sequencing
02-19-2019, 09:04 AM
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Replies: 6
Views: 6,921
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Forum: RNA Sequencing
02-19-2019, 08:52 AM
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Replies: 6
Views: 6,921
STAR read Mapping
Hello everybody,
I kindly need your help again ...
I want to map my reads on the genome using STAR but for some reason I get an error that I don't know how to solve
When I type the command...
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Forum: RNA Sequencing
02-15-2019, 08:49 AM
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Replies: 2
Views: 1,454
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Forum: RNA Sequencing
02-14-2019, 10:14 AM
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Replies: 2
Views: 1,454
FastQC and firefox
Hello everyone,
I want to perform a quality control of a fastq file.
so I run this line
patrizio$ fastqc --outdir raw/ raw/SRR359063_1.fastq.gz
and I have this
Analysis complete for...
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Forum: RNA Sequencing
02-13-2019, 09:13 PM
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Replies: 4
Views: 2,829
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