Bioinformatics Answers (original) (raw)

Comment: Lucidea Array Spotter - Question about machinery byTaylor • 0

Thank you so much!

Comment: Lucidea Array Spotter - Question about machinery byGenoMax 151k

This is a microarray spotting/printing machine that was likely used to "print" oligos (complementary to specific genes etc) on array substr…

Comment: How to generate identiy score between aligned sequences with Mauve? byGenoMax 151k

> ERROR ~ No such file or directory: /home/gigiux/Downloads/ALIGN/target_genome_file.fa Looks like the error is now with a different file.

Comment: Create local Blast database alias with blastdb_aliastool fails byGenoMax 151k

You can use `blastdbcmd` to retrieve data from pre-formatted databases. An example that is supposed to retrieve `gi` numbers is the command…

Comment: Deduplication rate of shotgun metagenomes using fastqc byvikasmh111 • 0

Thank you, will try and check.

Comment: How to generate identiy score between aligned sequences with Mauve? bymarongiu.luigi ▴ 740

Thank you, I tried but this time I got: ``` ERROR ~ Validation of pipeline parameters failed! -- Check '.nextflow.log' file for details T…

Answer: Deduplication rate of shotgun metagenomes using fastqc byGenoMax 151k

> Is fastqc a reliable tool for estimation of duplication of reads in metagenomes? While `FastQC` is a reliable tool because of the time/…

Answer: Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses byBastien Hervé 6.2k

I would inspect the `loadings` of the PCAs rather than a strict `PC1 vs. PC1v2`. Check first if the genes driving PC1 are the same as the o…

Comment: Need help to perform survival analysis byYugan Gogul Muthukumar ▴ 10

You have to state it clearly regarding what's your objective and what's your problem, if you're facing an error describe the error and ask …

Comment: Create local Blast database alias with blastdb_aliastool fails byetienne • 0

Thank you. How do you checked the GI with the N/A response? Is there a way to alias using accession numbers? Or taxID? I need to make a da…

Comment: Best choices for DGE and pathway enrichment analysis in single cell data using p bytxema.heredia ▴ 210

Thank you for your insights! Yes, I also lack formal stats education. I tend to use simple tests because they are easier to interpret (bot…

Answer: How can I find KO IDs for ORF sequences in a large FASTA file? byMensur Dlakic ★ 29k

There is a tool made exactly for that purpose: https://github.com/takaram/kofam\_scan

Answer: Normalization - Tissue specificity analysis byPallavi • 0

They develop TransTEx to look at Tissue specific transcripts. Check out their database. [TransTEx][1] [1]: https://academic.oup.c…

Answer: Transcript Specific Expression Data byPallavi • 0

We developed TransTEx to look at Tissue specific transcripts [TransTEx][1] [1]: https://academic.oup.com/bioinformatics/article/40/8/…

Answer: Database To Look For Tissue-Specific Transcript Expression Of The Same Gene. byPallavi • 0

We developed TransTEx to look at Tissud specific transcripts [TransTEx][1] [1]: https://academic.oup.com/bioinformatics/article/…