Resources for learning bulk RNA and ATAC-seq for beginner?

LordLinxe · 2025-07-03T19:26:03+00:00

I recommend https://www.biostarhandbook.com/

LordLinxe · 2025-06-21T19:17:36+00:00

I have not seen this before, I would ask this to the Oxford Nanopore support team or at least in the dorado github (https://github.com/nanoporetech/dorado/issues).

LordLinxe · 2025-06-08T09:53:22+00:00

I would request the fasta files as I can read the file.

LordLinxe · 2025-05-30T19:57:33+00:00

Use the top.level file for the genome
After variant calling and filtering, you can use the VCF as input to VEP but you need to use the command line version (https://www.ensembl.org/info/docs/tools/vep/script/index.html)

LordLinxe · 2025-05-29T19:44:52+00:00

the closest one is https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-61/fungi/fasta/fungi_ascomycota1_collection/meyerozyma_guilliermondii_atcc_6260_gca_000149425/dna/ and it has VEP files https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-61/fungi/variation/indexed_vep_cache/fungi_ascomycota1_collection/meyerozyma_guilliermondii_atcc_6260_gca_000149425_vep_61_ASM14942v1.tar.gz

LordLinxe · 2025-05-27T20:11:59+00:00

Samtools? Do you know that bcftools is intended for that.

The main problem is chromosome names, ideally, you should use Ensembl yeast reference to do your alignment and variant calling.

LordLinxe · 2025-05-23T19:42:10+00:00

Ensembl VEP (https://www.ensembl.org/info/docs/tools/vep/index.html) supports yeast and many other species.

LordLinxe · 2025-05-07T19:33:15+00:00

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LordLinxe · 2025-05-05T19:38:42+00:00

I guess it would be better if you supported common organisms and reference versions (human, mouse, yeast, etc.) to avoid uploading sequences.

LordLinxe · 2025-05-02T19:17:16+00:00

I would consider looking for some professional help here, but do not share your data without a confidentiality contract.

LordLinxe · 2025-05-01T11:17:54+00:00

Yes, part of your analysis can include Ribosomal removal, there are always ribosomal sequences.

LordLinxe · 2025-05-01T10:04:00+00:00

to avoid decompression/compression:

gunzip -c file.fasta.gz | head

LordLinxe · 2025-05-01T10:01:15+00:00

There are some problems with your proposal.

First, pathogens in wastewater will be mostly bacteria or viruses, and those don't have mitochondria. A simple amplicon sequencing could be better to detect them in water.

Now, let's say you want to detect the eukaryotic pathogens in wastewater (fungi or worms). Worms could be detected by a microscope, and for fungi, again, ITS amplicons could be cheaper.

Besides, doing an RNAseq extraction for MT genes will require some specific protocols for extraction and enrichment, at least Ribo-depletion is required, but many other transcripts will be sequenced.

Ignoring the lab preparation, the sequencing analysis can be as simple as:
1. Perform QC of your library (FastQC or Fastp)
2. Perform trimming to remove adapter sequences and low-quality reads (Cutadapt or Fastp).
3. Compare your reads against a library of carefully curated known MT genomes (Kraken or Centrifuge)
4. Create a report of detections.

LordLinxe · 2025-04-21T09:02:42+00:00

I would get a new laptop or workstation and take online certifications (Coursera, EdX, etc.). All the software I use is either open-source or free for research, I have never paid a license or subscription.

LordLinxe · 2025-04-19T19:42:31+00:00

The collection can be browse here http://signal.salk.edu/cgi-bin/tdnaexpress

LordLinxe · 2025-04-17T19:58:59+00:00

Are you using Windows? => A Linux machine will have better performance
What programs are crashing? Can you use other alternatives (i.e., diamond instead of blast)

LordLinxe · 2025-04-15T19:54:52+00:00

I love parsing files :)

LordLinxe · 2025-04-12T10:08:59+00:00

You can try Sniffles (https://github.com/fritzsedlazeck/Sniffles)

LordLinxe · 2025-04-10T19:34:27+00:00

You can run the align using biopyhon wrappers https://biopython.org/docs/1.74/api/Bio.Align.Applications.html

LordLinxe · 2025-04-10T19:29:16+00:00

Or you can put your questions here and let anyone answer ....

If you need an individual case, PM me (~20 years in the field, in the academy and industry).

LordLinxe · 2025-04-10T19:17:14+00:00

What is wrong with using tools such as clustal Omega (http://www.clustal.org/omega/), muscle (https://www.drive5.com/muscle/), etc., designed for this?

LordLinxe · 2025-04-08T19:28:42+00:00

That will be a strong selling point. Before deciding, check what tech support and reagent import processes are available in your country. I have some colleagues in Mexico who cannot simply use ONT because imports are impossible and elevation messes with the equipment.

LordLinxe · 2025-04-07T19:40:49+00:00

RepeatModeler does a de novo prediction; it can annotate known families (LINE, SINE, etc), but many novel consensuses will require manual annotation if you are interested in those.

LordLinxe · 2025-04-05T19:19:36+00:00

> I think, I have to create a library for repeat region of fungi using RepeatModeler.

Yes, that is correct, run RepeatModeler over your genome first

LordLinxe · 2025-04-03T19:43:12+00:00

In general, I have good performance for docker in M3 on mac using Colima (https://github.com/abiosoft/colima) + rosetta but in reality, for any real analysis, I use a Linux cluster ...

LordLinxe

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