User: bioinfo8

gravatar for bioinfo8
bioinfo890
Reputation:
90
Status:
Trusted
Location:
Last seen:
2 days, 20 hours ago
Joined:
1 year, 9 months ago
Email:
g***************@gmail.com

Posts by bioinfo8

<prev • 145 results • page 1 of 15 • next >
0
votes
1
answer
154
views
1
answer
Extract gene ids from DESeq2 result dataframe for specific comparison based on vennDiagram
... Hi everyone, I have used the code mentioned [here][1] to generate Venn diagram from `DESeq2` pairwise analysis. 1) I can see 124 genes specific to OPvsLL.33 from the venn diagram (Figure 2) and would like to extract them from DESeq2 result dataframe (already annotated with ensembl) by using entrez ...
venndiagram deseq2 limma rna-seq venn written 12 days ago by bioinfo890 • updated 6 days ago by Kevin Blighe9.3k
0
votes
1
answer
163
views
1
answers
Comment: C: Error while running clusterProfiler
... I figured out and it worked: gene_char <- as.character(gene$entrezgene) ggo <- clusterProfiler::groupGO(gene = gene_char, OrgDb = org.my_species.eg.db, ont = "BP", level = 3, readable = TRUE) ...
written 21 days ago by bioinfo890
0
votes
1
answer
163
views
1
answers
Comment: C: Error while running clusterProfiler
... Thanks for the hint. I managed to solve. But now, getting another error from the same command [Guangchuang Yu][1] : Error in validObject(.Object) : invalid class “groupGOResult” object: invalid object for slot "gene" in class "groupGOResult": got class "data.frame", should be or extend c ...
written 25 days ago by bioinfo890
1
vote
1
answer
163
views
1
answer
Error while running clusterProfiler
... Hi, I am trying to run clusterProfile after installing all dependencies and when I run: ggo <- clusterProfiler::groupGO(gene = gene, OrgDb = org.db, ont = "BP", level = 3, readable = TRUE) I get the following error: Error in rsqlite_send_query(conn@ptr, statement) : external po ...
R clusterprofiler rna-seq written 25 days ago by bioinfo890 • updated 25 days ago by Guangchuang Yu1.6k
2
votes
1
answer
206
views
1
answer
featureCounts for paired bam files and dealing with multimapping reads?
... Hi, I have multiple paired-end bam files from rnaseq experiments (hisat2 aligned). I extracted properly-paired reads, sorted, indexed and ran featureCounts using the following command (as per http://bioinf.wehi.edu.au/featureCounts/): featureCounts -p -t exon -g gene_id -a species.gtf -o bam.f ...
paired featurecounts rna-seq multimapping reads written 6 weeks ago by bioinfo890 • updated 6 weeks ago by Devon Ryan74k
0
votes
11
answers
111k
views
11
answers
Comment: C: Tools To Calculate Average Coverage For A Bam File?
... @[genomax][1] My bam files are very big and `Qualimap` has not been helpful, so as `bbmap` which is Java-based (memory issues like `Picard` and `QoRTs`) and hence I used `samtools depth`. My depth files are also in GB. [1]: https://www.biostars.org/u/18713/ ...
written 8 weeks ago by bioinfo890
0
votes
11
answers
111k
views
11
answers
Comment: A: Tools To Calculate Average Coverage For A Bam File?
... Hi, I have multiple paired-end bam files from RNA-Seq data, already aligned and computed depth with `samtools depth > bam.depth`. Would any one please guide for any straight forward/latest way to compute coverage plots, avg. coverage plots and other metrics from depth files? `Picard CollectRNAs ...
written 8 weeks ago by bioinfo890
0
votes
11
answers
111k
views
11
answers
Comment: C: Tools To Calculate Average Coverage For A Bam File?
... @[Jorge Amigo][1] samtools depth *bamfile* | awk '{sum+=$3} END { print "Average = ",sum/NR}' by @[russdurrett][2] also gives same output for my paired-end bam file from RNA-Seq:-) [1]: https://www.biostars.org/u/375/ [2]: https://www.biostars.org/u/7480/ ...
written 8 weeks ago by bioinfo890
0
votes
1
answer
190
views
1
answer
RSeQC installation error
... Hi, I am trying to install RSeQC as per [instructions][1], but getting following error : $python setup.py install --root=$HOME/.local/bin Unable to find pgen, not compiling formal grammar. Compiling /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Plex/Scanners.py because it changed. ...
python ngs qc rseqc written 8 weeks ago by bioinfo890 • updated 8 weeks ago by h.mon9.8k
0
votes
1
answer
190
views
1
answers
Comment: C: Error in running QoRTs after hisat2 alignment
... @[h.mom][1] I tried with -Xmx64g, but same error. I don't want to sort bam by name as it will take so longer and I have multiple files. [1]: https://www.biostars.org/u/6093/ ...
written 8 weeks ago by bioinfo890

Latest awards to bioinfo8

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Sleuth: Combined lrt and wt tests, clustered heatmap
Voter 3 months ago, voted more than 100 times.
Centurion 4 months ago, created 100 posts.
Supporter 7 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1297 users visited in the last hour