User: dina.hesham139

Reputation:
80
Status:
Trusted
Location:
Egypt
Last seen:
2 months, 2 weeks ago
Joined:
3 years, 5 months ago
Email:
d*************@gmail.com

Posts by dina.hesham139

<prev • 46 results • page 1 of 5 • next >
0
votes
0
answers
76
views
0
answers
Astalavista landscape AS gtf file output
... Hi, Have anyone tried Astalavista for alternative splicing analysis? If yes, how do I proceed after obtaining the LandscapeAS.gtf file? Thanks in advance! ...
astalavista rna-seq written 11 weeks ago by dina.hesham13980
0
votes
0
answers
153
views
0
answers
Comment: C: ASPLI (RNAseq AS) R package error
... bam files ranges 6-8gb. I analyze 2 at a time I used windows at first of 8gb RAM. Then I analyzed the data using a macbook pro 256, 2.3 GHz, 8 GB RAM. Also, gave me a memory error! ...
written 11 weeks ago by dina.hesham13980
0
votes
0
answers
153
views
0
answers
ASPLI (RNAseq AS) R package error
... Hi, I'm using ASPLI (An integrative R package for analysing alternative splicing) to study RNAseq data. Whenever I try to load the bam files I get this error: Error in value[[3L]](cond) : 'Realloc' could not re-allocate memory (167772160 bytes) file: WT_C1.bam index: NA Any ...
R rna-seq aspli written 12 weeks ago by dina.hesham13980 • updated 11 weeks ago by RamRS17k
0
votes
2
answers
527
views
2
answers
Comment: C: Alternative splicing analysis following kallisto?
... Thanks alot Istvan ! What other pipeline would you recommend for studing alternative splicing? esp. for rice and in my case I have a condition that doesn't have a replicate (i.e. I can't use rMATS for example!)? ...
written 5 months ago by dina.hesham13980
0
votes
0
answers
216
views
0
answers
AStalavista for rice alternative splicing analysis?
... Hi, Did anyone try AStalavista for alternative splicing analysis, esp.for rice RNASeq data? Does it manage to work if one of the conditions doesn't have a replicate? (a major drawback to rMATS!!) Is there a tutorial to follow? Thanks in advance! ...
rna-seq alternative splicing written 5 months ago by dina.hesham13980
6
votes
2
answers
527
views
2
answers
Alternative splicing analysis following kallisto?
... Hi, I used Kallisto for analyzing Rice RNAseq data, is there any tool that I can use to study alternative splicing following kallisto, a tool that doesn't require bam files and supports Rice genome? Thanks in advance! ...
kallisto rna-seq alternative splicing written 5 months ago by dina.hesham13980 • updated 5 months ago by kristoffer.vittingseerup470
0
votes
1
answer
205
views
1
answers
Comment: C: RNAseq Rice: multiple condition testing and annotation
... Thank you! I will give it a try! ...
written 6 months ago by dina.hesham13980
0
votes
1
answer
205
views
1
answer
RNAseq Rice: multiple condition testing and annotation
... Hello, I'm working on Rice rnaseq data. Kallisto was used for the pseudo-alignment. I have to questions: 1- I have 6 conditions 2 replicates each (12 samples in total), how can I do multiple condition testing to get the differential expressed genes? I tried sleuth and deseq2 but I couldn't do all ...
rice rna-seq written 6 months ago by dina.hesham13980 • updated 6 months ago by h.mon19k
0
votes
1
answer
504
views
1
answers
Comment: C: "makeTxDbFromGFF" error ?!
... I re-installed all the packages and the error is not yet resolved! ...
written 10 months ago by dina.hesham13980
2
votes
1
answer
504
views
1
answer
"makeTxDbFromGFF" error ?!
... Hey, I'm using deseq2 after kallisto to analyze rice data. I'm using an ensembl gtf and I want to create a txdb. I used this one: txdb2 <- makeTxDbFromGFF(file="C:/Users/Dee/Desktop/Thesis_rice/Oryza_sativa.IRGSP-1.0.37.gtf", format=("gtf"), dataSource=paste("ftp://ftp.ensemblgenomes.org/pub ...
tximport rna-seq written 10 months ago by dina.hesham13980 • updated 10 months ago by Bastien Hervé1.8k

Latest awards to dina.hesham139

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Annotation file (gff3) for hg38 to be used with MISO
Popular Question 3 months ago, created a question with more than 1,000 views. For Annotation file (gff3) for hg38 to be used with MISO
Epic Question 3 months ago, created a question with more than 10,000 views. For HISAT2 command help
Popular Question 4 months ago, created a question with more than 1,000 views. For Annotation file (gff3) for hg38 to be used with MISO
Popular Question 6 months ago, created a question with more than 1,000 views. For Annotation file (gff3) for hg38 to be used with MISO
Popular Question 7 months ago, created a question with more than 1,000 views. For Annotation file (gff3) for hg38 to be used with MISO
Popular Question 9 months ago, created a question with more than 1,000 views. For From HISAT2 to cuffdiff?
Popular Question 9 months ago, created a question with more than 1,000 views. For Is there a way to add xs tag to a sam file?
Great Question 18 months ago, created a question with more than 5,000 views. For HISAT2 command help
Great Question 18 months ago, created a question with more than 5,000 views. For hg38 annotation file (gtf) UCSC format
Popular Question 18 months ago, created a question with more than 1,000 views. For Is there a way to add xs tag to a sam file?
Popular Question 18 months ago, created a question with more than 1,000 views. For Can I use sorted bam files from STAR with Stringtie?
Popular Question 18 months ago, created a question with more than 1,000 views. For HISAT2 command help
Popular Question 2.2 years ago, created a question with more than 1,000 views. For HISAT2 command help
Popular Question 2.4 years ago, created a question with more than 1,000 views. For HISAT2 command help

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 683 users visited in the last hour