Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In

User: Sam

gravatar for Sam
Sam • 80
Reputation:
80
Status:
Trusted
Location:
Last seen:
1 week ago
Joined:
1 year, 1 month ago
Email:
V**********@gmail.com

Posts by Sam

<prev • 129 results • page 1 of 13 • next >
0
votes
0
answers
109
views
0
answers
Comment: C: non-integer numReads for differential expression analysis
... I don't have gft file for my db, in that case can I use the tximport ? ...
written 11 days ago by Sam • 80
0
votes
0
answers
109
views
0
answers
non-integer numReads for differential expression analysis
... Dear All I want to find predicted lncRNA expression according to RNA-seq data, I prepared a database from all of the predicted lncRNA and then I aligned the PE RNA-seq libs to the indexed lncRNA db via salmon. but in salmon output files there is some non-integer numReads, what is the best approach ...
non-integer numreads deseq2 written 12 days ago by Sam • 80
0
votes
3
answers
204
views
3
answers
Comment: C: compare two file to retrieve common lines
... in the files some of the name are in this format scaffold_1005 6522 scaffold_1005 6565 scaffold_1006 12174 but in out put file they change to : scaffold 1006_12174 scaffold 1005_6565 which means name and position have been merged. how I can solve it ...
written 19 days ago by Sam • 80
10
votes
3
answers
204
views
3
answers
compare two file to retrieve common lines
... Dear ALL I have two tab file: file 1 Chromosome Position Chr01 45943 Chr01 45965 Chr01 45981 Chr01 46122 Chr02 45965 file 2 Chr01 6789 SNP A T 15.17 90.91 6 18 6 Chr01 6795 SNP G T 12.11 81.82 6 ...
bash awk written 20 days ago by Sam • 80
0
votes
0
answers
137
views
0
answers
Comment: C: cufflinks large bundles warning
... Thanks for your help, but with this warning, the processing time of cufflinks increased at least 10 times. ...
written 5 weeks ago by Sam • 80
0
votes
0
answers
137
views
0
answers
Comment: C: cufflinks large bundles warning
... but I tried also(the same lib ) with Tophat2 and Hisat2 and cufflinks worked well without any warning and error. should I change any flag in the star to be compatible with cufflinks? ...
written 5 weeks ago by Sam • 80
1
vote
0
answers
137
views
0
answers
cufflinks large bundles warning
... Dear All I used star to align the PE lib with this command and then I converted sam file to bam and sorted it with samtools but after running the cufflinks I got "Warning: Skipping large bundle" how I can fix it ? Thanks STAR --runThreadN 12 --genomeDir /genome_index_star -sjdbGTFfile /gen ...
cufflinks star written 6 weeks ago by Sam • 80
0
votes
0
answers
126
views
0
answers
what is the easiest/fastest way to convert from BAM to GTF
... I converted the output of STAR to BAM and for the next step I need to convert it to GTF, so what is the easiest/fastest way to convert from BAM to GTF? Thanks ...
gtf bam written 6 weeks ago by Sam • 80
0
votes
0
answers
252
views
0
answers
Comment: C: plotting according p-value
... we have some positions which are significant differences with the Mendelian ratio and I think the simplest way to visualize the result is showing them with a plot. du to that I mentioned to "in a plot similar to volcano plot for gene expression" to quickly identify changes in large data sets and a ...
written 6 weeks ago by Sam • 80
0
votes
0
answers
252
views
0
answers
Comment: C: plotting according p-value
... could you help me to have the 3D plot for this data? ...
written 6 weeks ago by Sam • 80

Latest awards to Sam

Popular Question 3 months ago, created a question with more than 1,000 views. For bash and awk code
Supporter 6 months ago, voted at least 25 times.
Centurion 7 months ago, created 100 posts.
Rising Star 12 months ago, created 50 posts within first three months of joining.
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1976 users visited in the last hour