User: bioinfo8

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bioinfo890
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Posts by bioinfo8

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Comment: C: Fundamentals Of Designing Biological Databases?
... [Jean-Karim Heriche][1] I would like to store information on a protein family among different organisms including their names, gene information, sequence information, structure etc. Would you please elaborate more on access pattern? [1]: https://www.biostars.org/u/2318/ ...
written 4 months ago by bioinfo890
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Answer: A: Fundamentals Of Designing Biological Databases?
... Hi all, I am looking for ways to create a biological database. I have some data in MS-Access and kind of confused on which approach I should follow to create database. I would like to have an updated opinion from the biostars community on the different ways of creating a database, front and back-en ...
written 5 months ago by bioinfo890
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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 6 months ago by bioinfo890 • updated 6 months ago by Kevin Blighe21k
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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 6 months ago by bioinfo890
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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 7 months ago by bioinfo890
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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 7 months ago by bioinfo890 • updated 7 months ago by Guangchuang Yu1.8k
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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 7 months ago by bioinfo890 • updated 7 months ago by Devon Ryan80k
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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 months ago by bioinfo890
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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 months ago by bioinfo890
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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 months ago by bioinfo890

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Popular Question 7 months ago, created a question with more than 1,000 views. For Sleuth: Combined lrt and wt tests, clustered heatmap
Voter 10 months ago, voted more than 100 times.
Centurion 10 months ago, created 100 posts.
Supporter 14 months ago, voted at least 25 times.

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