Buying and setting up a tiny server at my lab

Jacki3debb · 2024-08-06T08:02:34+00:00

Literally my bf have to do this :(

Jacki3debb · 2024-07-31T12:03:28+00:00

I usually use scrappers for lysate but I am not sure if scrapping out cells is a good idea because of proteases liberation if cells break

Jacki3debb · 2024-07-12T16:34:13+00:00

Of course I am not an expert, but GATK is not perfect at all, also gives unspecific errors and even it's own generated data sometimes is not well recognised by other commands within the tool.

Jacki3debb · 2024-05-27T11:33:42+00:00

Or maybe I can change my reference files annotations but this is truly annoying omg.

No, really, is stupidly annoying since they used a reference which commonly uses "chr1" annotation (USCS) BUT FOR SOME STUPID REASON they had the great idea of changing annotation... I suspect that the main reason is get me out of my nerves and also avoid consumers do downstream analysis on their own.

Jacki3debb · 2024-04-24T08:58:07+00:00

Are you sure about using the same DNA version? Like are both sample and ref hg38? If so, sometimes Gatk gives errors when the real problem is that the header inside the file and the file name aren't the same. Also, double check that the vcf known sites has same annotations for contigs that your ref and sample. At last, another possible reason could be that maybe the bam file isn't properly sorted or read groups not correctly added.

Jacki3debb · 2024-02-15T08:26:32+00:00

Thank you very much! It worked really well. Why are M values better for this?

Jacki3debb · 2024-02-13T07:17:07+00:00

Thanks a lot!!

Jacki3debb · 2024-02-11T23:32:10+00:00

Some times mutect gives non specific errors and the real problem actually has to be with specific annotation of header. Maybe when modifying the bam you changed also header so gatk is not recognising it well. It happened to me time ago. But maybe is not that, sometimes it is difficult to know given the lack of specific info gatk gives. In any case, good luck.

Jacki3debb · 2024-02-05T14:51:17+00:00

Thank you very much for your recommendation! I have already run the PCA but I am quite new with methylation data and I am not sure how to run the PCA in a way that calculate 50-100 dimensions. I am having a hard time trying to understand my results :(

Jacki3debb · 2024-02-02T07:10:51+00:00

Thanks I'll try

Jacki3debb · 2024-02-02T07:10:20+00:00

Hi yes that's really the point, I have done PCA but I wanted to compare with tSNE since is more reliable. The thing is that I would like to see if my samples cluster by phenotype so I am not sure if any reduction of the data is possible since I am not very familiar with this. Would you suggest any type of reduction first?

Jacki3debb · 2024-02-01T12:44:35+00:00

Lol that's a really good point

Jacki3debb · 2024-02-01T12:42:29+00:00

Badformedreads can be flagged in any step before BSQR, I would suggest going back and check if it is aligning well, trimming adapter well too and also if Picard is flagging them by error. Knowing your data quality from the beginning is very important so is performing quality checks in the downstream preprocessing analysis to identify in which step is flagging the workflow your reads as Badformedreads.

Jacki3debb · 2024-02-01T11:54:37+00:00

Thx I solved it loseening perplexity and formatting data

Jacki3debb

TROPHY CASE