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Forum: RNA Sequencing 04-18-2019, 05:22 AM
Replies: 0
Views: 1,073
Posted By NDUFB11
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 = ~...
Forum: RNA Sequencing 04-11-2019, 08:08 AM
Replies: 3
Views: 1,109
Posted By NDUFB11
ok maybe I got it, if someone wants to choose...

ok maybe I got it,
if someone wants to choose featureCounts does it otherwise can use the output file.tab of STAR :)
Forum: RNA Sequencing 04-11-2019, 08:03 AM
Replies: 3
Views: 1,109
Posted By NDUFB11
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...
Forum: RNA Sequencing 04-11-2019, 07:18 AM
Replies: 3
Views: 1,109
Posted By NDUFB11
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...
Forum: RNA Sequencing 04-09-2019, 10:38 AM
Replies: 4
Views: 1,342
Posted By NDUFB11
Hi sklages, I solved the problem by skipping...

Hi sklages,
I solved the problem by skipping TrascriptomeSAM,
running just this:

--quantMode GeneCounts

Thank you :)
Forum: RNA Sequencing 03-27-2019, 06:01 AM
Replies: 4
Views: 1,342
Posted By NDUFB11
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...
Forum: RNA Sequencing 03-26-2019, 06:46 PM
Replies: 4
Views: 1,342
Posted By NDUFB11
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...
Forum: RNA Sequencing 03-06-2019, 10:11 AM
Replies: 0
Views: 951
Posted By NDUFB11
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...
Forum: RNA Sequencing 03-05-2019, 07:59 AM
Replies: 5
Views: 1,026
Posted By NDUFB11
but if I use Deseq2 it requires biological...

but if I use Deseq2 it requires biological replicates, which I don't have it in my case.

How can I create the data frame and the condition with DESq2 in this case?

thank you
Forum: RNA Sequencing 03-05-2019, 07:44 AM
Replies: 5
Views: 1,026
Posted By NDUFB11
Thank you genoMax for your answer, can you...

Thank you genoMax for your answer,

can you tell me how this reads are normalized?

thanks
Forum: RNA Sequencing 03-05-2019, 06:50 AM
Replies: 5
Views: 1,026
Posted By NDUFB11
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?...
Forum: RNA Sequencing 02-24-2019, 09:09 PM
Replies: 2
Views: 964
Posted By NDUFB11
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.
...
Forum: RNA Sequencing 02-24-2019, 11:15 AM
Replies: 2
Views: 964
Posted By NDUFB11
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...
Forum: RNA Sequencing 02-22-2019, 03:31 AM
Replies: 0
Views: 871
Posted By NDUFB11
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...
Forum: RNA Sequencing 02-21-2019, 10:24 AM
Replies: 1
Views: 919
Posted By NDUFB11
ok I solved the problem by combining the two bam...

ok I solved the problem by combining the two bam files with this command line,

# Program:featureCounts v1.6.3; Command:"featureCounts" "-M" "--fraction" "-g" "gene_id" "-T" "4" "-s" "0" "-a"...
Forum: RNA Sequencing 02-21-2019, 06:53 AM
Replies: 1
Views: 919
Posted By NDUFB11
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...
Forum: RNA Sequencing 02-20-2019, 05:39 AM
Replies: 0
Views: 704
Posted By NDUFB11
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...
Forum: RNA Sequencing 02-19-2019, 10:15 AM
Replies: 2
Views: 860
Posted By NDUFB11
ok probably I solved the problem by using this...

ok probably I solved the problem by using this line command to install a older version of samtools

conda install -c bioconda samtools=1.9=h8ee4bcc_1


from this forum discussion

...
Forum: RNA Sequencing 02-19-2019, 09:59 AM
Replies: 2
Views: 860
Posted By NDUFB11
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...
Forum: RNA Sequencing 02-19-2019, 09:26 AM
Replies: 6
Views: 915
Posted By NDUFB11
It's working :D :D :D !!!! holeee'! have a...

It's working :D :D :D !!!! holeee'!

have a look

Patrizios-MBP:processing patrizio$ STAR --genomeDir genome/star/ --runThreadN 4 --readFilesIn clipped/SRR359063_1.fastq...
Forum: RNA Sequencing 02-19-2019, 09:04 AM
Replies: 6
Views: 915
Posted By NDUFB11
Do you think that this is the reason why I have...

Do you think that this is the reason why I have this error? this is a nematode genome so I thought the process would have been faster than human

I will scan the command, I found an error probably...
Forum: RNA Sequencing 02-19-2019, 08:52 AM
Replies: 6
Views: 915
Posted By NDUFB11
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...
Forum: RNA Sequencing 02-15-2019, 08:49 AM
Replies: 2
Views: 819
Posted By NDUFB11
I did it :) Thank you -P

I did it :)

Thank you

-P
Forum: RNA Sequencing 02-14-2019, 10:14 AM
Replies: 2
Views: 819
Posted By NDUFB11
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...
Forum: RNA Sequencing 02-13-2019, 09:13 PM
Replies: 4
Views: 1,055
Posted By NDUFB11
Thumbs up It worked :) thank you!!

It worked :)

thank you!!
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