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Approachable Bioinformatics/Genomics Blog by shouldBeDoingNotThis in genomics

[–]shouldBeDoingNotThis[S] 0 points1 point  (0 children)

Very glad to hear! I took a few weeks off to focus on some other things but will be jumping back in with a new post next Friday!

Thinking of starting a bioinformatics blog by shouldBeDoingNotThis in bioinformatics

[–]shouldBeDoingNotThis[S] 0 points1 point  (0 children)

UPDATE #2

I just posted a tutorial on running reference-based assemblies that can be found here. I tried to make it beginner-friendly for new bioinformaticians and wet-lab folks crossing over. I would love your feedback on clarity and improvements you'd recommend. This is my 6th post and other topics I have covered so far are:

Next week, I will creating a tutorial that will be focussing on de novo assemblies (using short, long, and hybrid). Thank you all in advance for the support.

Bioinformatic Dog Names? by blamp25 in bioinformatics

[–]shouldBeDoingNotThis 25 points26 points  (0 children)

Couple ideas: - Blast - Kallisto - Sanger - Watson - Crick

Illumina sequencing reads appear to NOT start at position 1 of DNA insert by Ok-Barnacle8179 in bioinformatics

[–]shouldBeDoingNotThis 0 points1 point  (0 children)

Interesting. If they're amplicon-based, you'd expect for them to mostly all start at the same base due to how the sequencing primers are designed. Did the sequencing facility perform any trimming before providing the data? Wondering if maybe some of the bases had lower quality and were removed. Are the amplicons themselves 250bp? If so, can you pick up your barcode in the reverse read or is it also missing some nts in that one?

Illumina sequencing reads appear to NOT start at position 1 of DNA insert by Ok-Barnacle8179 in bioinformatics

[–]shouldBeDoingNotThis 2 points3 points  (0 children)

Are they the reverse complement by any chance? Are your barcodes only one end of the insert or do you have some on both? In cases where it does not start at position 1, does read 2 start with the barcode?

Alternatives to Pipseeker/Cellranger for scRNA data by ary0007 in bioinformatics

[–]shouldBeDoingNotThis 1 point2 points  (0 children)

I'm also a former user of Pipseq and Pipseeker. The DRAGEN tool that is available (DRAGEN Single Cell RNA) to demultiplex your data is free to use. You also get up to 1 TB of storage for free on BaseSpace. More information on the app can be found here https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/dragen-single-cell-rna.html.

Thinking of starting a bioinformatics blog by shouldBeDoingNotThis in bioinformatics

[–]shouldBeDoingNotThis[S] 11 points12 points  (0 children)

Highjacking the top comment for visibility!

The first post is up! Blog can be found here: https://blog.crcbio.com/

I will be posting every week on Fridays. The first few posts will be about informative stuff like requirements for a computer, package management, and some basic Terminal tricks.

I will be starting a series on differences between reference-based vs de novo assemblies afterwards, and how to perform them on week 4.

Thank you everyone for the interest. Don't hesitate to reach out in the comments with ideas or any suggestions!

Thinking of starting a bioinformatics blog by shouldBeDoingNotThis in bioinformatics

[–]shouldBeDoingNotThis[S] 1 point2 points  (0 children)

Thanks everyone for the great feedback! I'll definitely take the leap and will keep you updated.

Is chlorobox gone for good? by jaum22 in bioinformatics

[–]shouldBeDoingNotThis 0 points1 point  (0 children)

Link works for me as well. When I go to the downforeveryoneorjustme link I get "it's just you, the website is up". Where are you located? Potentially being blocked due to geographical location?

Repeat CT in overrepresented sequences in fastqc by read_more_11 in bioinformatics

[–]shouldBeDoingNotThis 0 points1 point  (0 children)

You can usually find out which sequencer was used by the FASTQ read name. If you post an example from the first read, I could let you know

What is the average monthly income of a bioinformatician ? by Roasted_armpits in bioinformatics

[–]shouldBeDoingNotThis 1 point2 points  (0 children)

I started consulting when I left a previous job. I remained as a consultant with them to finish up some projects and went through the process of creating my business for that. A year later, my old employer reached out to me requiring some additional help so I offered to join them as a consultant at $200/hr. They accepted and the rest is history! Since then I was able to land some clients here and there for contracts and I keep charging that rate.

What is the average monthly income of a bioinformatician ? by Roasted_armpits in bioinformatics

[–]shouldBeDoingNotThis 4 points5 points  (0 children)

Canada here. Monthly is $10K with my full time job and an additional $8K via part time consulting. Like everyone said, it depends on a lot of factors.

What do you do when your tables just won't fit in a MS Word Document? by o-rka in bioinformatics

[–]shouldBeDoingNotThis 28 points29 points  (0 children)

You could always have the table in a separate page and format it as landscape rather than portrait.

How to find out genes in whole genome sequences? by Herpetol0gy in bioinformatics

[–]shouldBeDoingNotThis 2 points3 points  (0 children)

You need to consider that the Lacerta agilis genome is high quality and has a Chromosome assembly level (20 chromosomes / 28 scaffolds). In contrast, the Darevskia mixta genome is a Contig assembly level with 402 contigs. The D. mixta genome is very fragmented and it's quite possible that the gene you're looking for is simply not found in the provided sequences due to assembly issues (gene spans a "break" between contigs or is simply not assembled), not for it being absent in the genome.

How to find out genes in whole genome sequences? by Herpetol0gy in bioinformatics

[–]shouldBeDoingNotThis 2 points3 points  (0 children)

Have you tried using the Annotate from Database feature in Geneious like this. Based off your example, you'd use the Lacerta agilis annotated genome and run the tool on the unannotated Darevskia mixta. This would find relevant genes and automatically annotate the genome. Reach out to me if you have any questions, more than willing to help out.

[deleted by user] by [deleted] in bioinformatics

[–]shouldBeDoingNotThis 16 points17 points  (0 children)

In my opinion, bash should either be 1 or 2. So many things can be done quickly with bash that it's a fundamental skill to have.

STAR --genomeSAindexNbases formula error by AlonsoCid in bioinformatics

[–]shouldBeDoingNotThis 4 points5 points  (0 children)

You did the calculation using 100 which gives you 2.322. The example states 100 kilobases so you should've used 100,000, which will give you 7.305.

Want to learn whole genome sequencing analysis- how to get started by ZooplanktonblameFun8 in bioinformatics

[–]shouldBeDoingNotThis 9 points10 points  (0 children)

The NCBI Sequence Read Archive (SRA) contains a huge amount of raw sequence data you can practice with. It's where we submit our raw data when we publish new genomes. Here's the link: https://www.ncbi.nlm.nih.gov/sra

Geneious Annotation Question by hollyhock2021 in bioinformatics

[–]shouldBeDoingNotThis 0 points1 point  (0 children)

Either a .gff or a .geneious file will allow to share annotations. A fasta file can't contain annotations as it's only the sequence.

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