User: sangita_b

gravatar for sangita_b
sangita_b70
Reputation:
70
Status:
Trusted
Location:
United Kingdom
Last seen:
1 year, 9 months ago
Joined:
4 years ago
Email:
s********@hotmail.co.uk

Posts by sangita_b

<prev • 14 results • page 1 of 2 • next >
0
votes
0
answers
1.5k
views
0
answers
Comment: C: error installing cummerbund in R studio
... Thank you. I have tried this, the following error comes up Error: package or namespace load failed for ‘RSQLite’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘digest’ ...
written 21 months ago by sangita_b70
0
votes
0
answers
1.5k
views
0
answers
Comment: C: error installing cummerbund in R studio
... Thank you, I have done this. How do I install digest to R? ...
written 21 months ago by sangita_b70
2
votes
0
answers
1.5k
views
5 follow
0
answers
error installing cummerbund in R studio
... Hi I have installed R (for Windows) and R studio (desktop version). I am trying to install cummerbund however the package won't install. I have tried a number of things based on forum posts but nothing has worked so far- can anyone offer any advice? Please see script for details: R version 3.4. ...
r studio cummerbund error written 21 months ago by sangita_b70 • updated 19 months ago by Biostar ♦♦ 20
0
votes
1
answer
3.5k
views
1
answers
Comment: C: Error: Could not find Bowtie 2 index files (p.*.bt2)
... Thanks Devon. I have added the  "-" in "-p 5" and now it works. it's always something small! ...
written 3.2 years ago by sangita_b70
1
vote
1
answer
3.5k
views
1
answers
Comment: C: Error: Could not find Bowtie 2 index files (p.*.bt2)
... I trimmed my fastq files and noticed that when aligning these files the concordant alignment rate was 0.4% (for my other samples the alignment rate was 90-92%). Long story short I am repeating the alignments and want to use the same version of TopHat that I used originally (I am worried that the tr ...
written 3.2 years ago by sangita_b70
3
votes
1
answer
3.5k
views
1
answer
Error: Could not find Bowtie 2 index files (p.*.bt2)
... Hi, I am repeating alignments using TopHat, I am using the same Bowtie index as I used previously (i.e I have successfully aligned reads using this index) My command line is below: tophat p 5 -G /home/msxakk/Desktop/NOT-BACKED-UP/iGenomes/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf -o ...
rna-seq written 3.2 years ago by sangita_b70 • updated 3.2 years ago by Devon Ryan88k
0
votes
2
answers
1.7k
views
2
answers
DESEQ2: How can I convert ensembl gene id's to HGNC gene names.
... Hi I have used DESeq2 to carry out differential gene expression analysis. My DESeq output contains ensembl gene id's. Is there a tool/ software package that I can use to convert these id's to gene names? I have tried Biomart however it cannot convert the id's for the whole file (>60,000) Thank ...
software ensembl id deseq2 gene id rna-seq written 3.4 years ago by sangita_b70 • updated 3.4 years ago by Martombo2.4k
0
votes
0
answers
1.4k
views
0
answers
error when using sickle for quality trimming
... Hi I have used  scythe to trim adapters and am now using sickle to quality trim. 1 out if 20 files has come with the error below (19/20 seem to be fine). Can anyone suggest why this is happening and how I can solve this issue? Thanks Sangita   msxsb3@msngs:~/projects/uPAR_overexp/2a_D1_E4_EV_24 ...
sickle quality trimming error rna-seq written 3.7 years ago by sangita_b70 • updated 3.5 years ago by Biostar ♦♦ 20
0
votes
0
answers
939
views
0
answers
Is it possible to use a self made txt doc containing normalised FPKM values in cuffdiff - for the purpose of multiple testing (calculate FDR / q value)
... I have used the Tuxedo pipeline to analyse my reads (RNASeq) for differential expression. The design of my experiment is: 5 conditiona (3 gene variants in an overexpression plasmid, empty vector control, and untransfected) replicated twice in two donors. The cells are primary human cells. After ...
rna-seq written 3.8 years ago by sangita_b70
0
votes
4
answers
1.4k
views
4
answers
Answer: A: using cufflinks when investigating differential expression
... Thanks Geek_y. Can I also ask if you know of programs that concatenate/ combine fastq files? Thanks ...
written 3.9 years ago by sangita_b70

Latest awards to sangita_b

Popular Question 3.2 years ago, created a question with more than 1,000 views. For Error: Could not find Bowtie 2 index files (p.*.bt2)
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Suggestions for RNA seq pipeline
Student 3.2 years ago, asked a question with at least 3 up-votes. For using cufflinks when investigating differential expression
Student 3.2 years ago, asked a question with at least 3 up-votes. For Suggestions for RNA seq pipeline

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1802 users visited in the last hour