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Forum: RNA Sequencing 03-06-2019, 10:11 AM
Replies: 0
Views: 177
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: 257
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: 257
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: 257
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: 366
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: 366
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: 296
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: 312
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: 312
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: 263
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: 335
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: 335
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: 5
Views: 329
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: 5
Views: 329
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: 5
Views: 329
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: 454
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: 454
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: 413
Posted By NDUFB11
Thumbs up It worked :) thank you!!

It worked :)

thank you!!
Forum: RNA Sequencing 02-13-2019, 12:12 PM
Replies: 4
Views: 413
Posted By NDUFB11
The suggestion turned out very useful and I'm...

The suggestion turned out very useful and I'm downloading the files.
I'm doing a course this days I wanted to practice and understand better by repeating what we did on my machine so it might be...
Forum: RNA Sequencing 02-13-2019, 11:24 AM
Replies: 4
Views: 413
Posted By NDUFB11
download with fastq-dump

Hello everyone, I'm still new to RNAseq and I hope I can find someone to help me out with my question.

I want to download RNAseq data (SRR) using SRA Toolkit which I already installed have on my...
Forum: Bioinformatics 07-11-2017, 01:31 PM
Replies: 8
Views: 1,132
Posted By NDUFB11
Dear GenoMax, I think I did another step...

Dear GenoMax,
I think I did another step forward, I run FutureCounts in R.
I used this command line:

> z <- featureCounts(fls, "hg19", nthreads = 30)

but it s not clear to me, how the...
Forum: Bioinformatics 07-11-2017, 07:36 AM
Replies: 1
Views: 523
Posted By NDUFB11
BAM alignment and counting

Hello everyone,
Can you tell me which is the most common way to quantify the reads from an RNAseq bam file?
Other that futureCounts, is there anything else well know and reliable?

Thanks
Forum: Bioinformatics 07-04-2017, 06:25 PM
Replies: 8
Views: 1,132
Posted By NDUFB11
Ok I tell you my story, I have R,...

Ok I tell you my story,

I have R, containing the package Rsubread::featureCounts() and I have two bam files which I named Cell1.bam and Cell2.bam.

I m in the directory where this files are
...
Forum: Bioinformatics 07-04-2017, 01:10 PM
Replies: 8
Views: 1,132
Posted By NDUFB11
Thank you genoMax, doesn t seem to be easy :/

Thank you genoMax, doesn t seem to be easy :/
Forum: Bioinformatics 07-03-2017, 12:19 PM
Replies: 8
Views: 1,132
Posted By NDUFB11
Hi Devon Ryan, Thank you for your answer, do...

Hi Devon Ryan,
Thank you for your answer, do you know where I can find a good tutorial that explains how to use featureCounts?

or if I can have the comman line

thanks
Showing results 1 to 25 of 27

 


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