User: Morris_Chair

gravatar for Morris_Chair
Morris_Chair50
Reputation:
50
Status:
Trusted
Location:
ISBReMIT
Last seen:
41 minutes ago
Joined:
1 year, 9 months ago
Email:
p********@operapadrepio.it

Posts by Morris_Chair

<prev • 57 results • page 1 of 6 • next >
0
votes
1
answer
107
views
1
answers
Comment: C: From StringTie to DESeq2
... Hi ATpoint, I answered to my self at some of your question, with low percentage I mean less the 20% of mapping unlike other tools with over 70% and the read lengh=101.
 I have human data, the final goal is to see which genes are upregulated or downregulate along with a set of genes of my interest ( ...
written 5 hours ago by Morris_Chair50
0
votes
1
answer
107
views
1
answers
Comment: C: From StringTie to DESeq2
... I tried salmon but I got low percentage of mapped reads for a sample, then I decided to go with stringtie.. I don't think to use ballgown anyways I have an OT: Do you think that DESeq2 and cummRbund do the same job? for example, can I with DESeq2 see the differential expression of specific genes ...
written 20 hours ago by Morris_Chair50
0
votes
1
answer
107
views
1
answers
Comment: C: From StringTie to DESeq2
... HI ATpoint, I have with me the paper "Transcript-level epxression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown", and for generating the table counts, shows the same command line of the link posted from you. stringtie -eB -G transcripts.gff What looks weird to me is th ...
written 1 day ago by Morris_Chair50
0
votes
1
answer
107
views
1
answers
Comment: C: From StringTie to DESeq2
... that's what I read and that's why there were the name of the samples in the first colum, just in case you need in the future they are needed ;) ...
written 1 day ago by Morris_Chair50
0
votes
1
answer
107
views
1
answers
Comment: C: From StringTie to DESeq2
... Hi Buffo, thanks for the answer but I get errors if I delete the first colum Error: Text file with sample ID and path invalid (/home/RNAseq/HISAT/BAM/sorted/Files.GTF/Treated_1.gtf) [@ws7910 Files.GTF]$ ...
written 1 day ago by Morris_Chair50
5
votes
1
answer
107
views
1
answer
From StringTie to DESeq2
... Dear all, After generating bunch of files with stringTie command line, I want to use DESeq2 for differential expression analysis. I understand that I have to create a matrix of read counts and the tool to use is prepDE.py, prepDE.py -i list_gtf.txt my output is 0 Treated_1 1 Treat ...
rna-seq written 1 day ago by Morris_Chair50 • updated 19 hours ago by Charles Warden6.5k
0
votes
0
answers
91
views
0
answers
Comment: C: Stringtie --merge and gtf_list.txt issue
... Hole' ! problem solved , I have this precious file ! Basically I had to specify the path into the txt file Thank you PS: my previous command line was used to generate every single file.txt from single BAM files ...
written 2 days ago by Morris_Chair50
0
votes
0
answers
91
views
0
answers
Comment: C: Stringtie --merge and gtf_list.txt issue
... Hi bioExplorer, here is the head of my gtf.txt file which is different than yours, did you put also the path beside of each? in my case the txt file is in the same folder of the gtf files so I think I should be ok [@ws7910 Files.GTF]$ head gtf_list.txt Treated_1.gtf Treated_2.gtf ...
written 2 days ago by Morris_Chair50
1
vote
0
answers
91
views
0
answers
Stringtie --merge and gtf_list.txt issue
... Hello guys, I’m having problems merging the GTF files generated with Stringtie. I know it must me a simple mistake that I m doing with the cmdline but also googling I couldn’t figure it out. The command line that I’m using for merging the files is this: stringtie --merge -G Homo_sapiens.GR ...
rna-seq written 2 days ago by Morris_Chair50
0
votes
1
answer
206
views
1
answers
Comment: C: HISAT2 reference genomes and starting code
... Lieven!!! probably I solved the issue !!!! geeze I can't believe! have a look please [@ws7910 RNAseq]$ hisat2 -q -x ./annotation/transcriptome/hisat2refgenes/grch37/genome -1 ./my_fastq/Treated_1_m1.fastq -2 ./my_fastq/Treated_1_m2.fastq -S sample.sam 680357 reads; of these: 680357 ...
written 4 days ago by Morris_Chair50

Latest awards to Morris_Chair

Popular Question 28 days ago, created a question with more than 1,000 views. For Bamfile first step analysis

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2204 users visited in the last hour