Awesome high quality bioinformatics video! We need more of these :)
@RayY-r4j
6 ай бұрын
FASTQ data need trimming.
@KatharineME
2 жыл бұрын
The CRAM file format is simply a newer and more compressed version of the BAM file format, for anyone who was wondering that :)
@programmer5350
2 жыл бұрын
Could you also do a video for the SLAM, JAM, and THANK YOU MA'AM file formats?
@cristianm7097
2 жыл бұрын
@@programmer5350 Are you already familiar with the WHAM-BAM file formats ?
@RohitSormaes
19 күн бұрын
Jackson Cynthia Wilson Gary Wilson Mark
@WsdcteHsdgxhte
Ай бұрын
Lewis Laura Thomas Sandra Harris Michelle
@secondeye3927
26 күн бұрын
thank you very much. this is so helpful and very clear to understand easily
@ZackarySmith-x2j
29 күн бұрын
Hall Gary Moore Shirley Young Maria
@wakeup9199
3 ай бұрын
Well done, bt still i have doubt!!! So if uploated vcf file in yfull and after that i upload da bam wht is da advantages??
@MrFilu13
27 күн бұрын
Good... 👍 Nicely explain ed
@stephenjohnson9733
22 күн бұрын
good explanation thanks
@europhile2658
Ай бұрын
excellent description!
@kaoulkae
2 жыл бұрын
This was very helpful and very well explained. You are talented 🙂
@arioche
Ай бұрын
great
@sinaisbitt
Жыл бұрын
Some great explanations in your videos. I'm really curious as to what we can do with the data once we get it. Right at the end of this video, you mentioned a video that would explain some of this. Do you still plan to make this?
@KatharineME
Жыл бұрын
Hi Simon! Yes I think what to do with the data is a question on everyone's mind who has had a DNA test. I do plan to make that video still. Stay tuned! If you want help in the short term, Guardiome does private custom DNA Analysis: www.guardiome.com/custom-dna-analysis.
@sapandeepsandhu4410
4 ай бұрын
SAM File Structure: Header Section: Optional, starts with '@', contains metadata about the sequence and the alignments. Alignment Section: Contains alignment information with each line representing a read. Columns in SAM: QNAME: Query template name. FLAG: Bitwise flag. RNAME: Reference sequence name. POS: 1-based leftmost mapping position. MAPQ: Mapping quality. CIGAR: CIGAR string. RNEXT: Reference name of the mate/next read. PNEXT: Position of the mate/next read. TLEN: Observed template length. SEQ: Segment sequence. QUAL: ASCII of Phred-scaled base quality+33.
@oksana03fel
2 жыл бұрын
Very clear video. Thank you. Katherine, could you please explain how to convert .fastq files to .vsf. Thank you
@sapandeepsandhu4410
4 ай бұрын
.FASTQ (Raw Sequence Data) FASTQ is a text-based format for storing both nucleotide sequences and their corresponding quality scores. It is widely used in high-throughput sequencing. File Structure: Header Line: Starts with '@' followed by a sequence identifier. Sequence Line: Contains the nucleotide sequence. Plus Line: Starts with a '+' and may be followed by the same sequence identifier. Quality Line: Contains quality scores for each nucleotide in the sequence, encoded as ASCII characters
@doctorkash0792
4 ай бұрын
Amazing explanation, really cleared up many things just by watching, thanks a ton and keep up the good work:)
@aleksandraperz5037
7 ай бұрын
Katharine, thank you so much for this video
@miguelarellano5260
Жыл бұрын
Thank you so much Katharine! you saved a biotech eng. student from Mexico! 🇲🇽
@deepap1307
5 ай бұрын
Thank you for the clear explanations of basics.
@iamadityavaishy
2 жыл бұрын
Thank you so much. You explained all this so easily 🤗🤩
@kikiarev
2 жыл бұрын
Thank you for the explanation! It's really confusing at first glance!
@NM-tx7zm
5 ай бұрын
This was excellently done and easy to follow! Thank you!
@eduardofernandezdelpeloso8663
Жыл бұрын
Nice video! do you know any software tool I can use to compare the results of full genome sequencing from two different companies? I have bought tests from Dante and Nebula, and once I get the results I would like to be able to compare them and do some statistical analysis of the differences.
@KristinaBecanovic
8 ай бұрын
thanks brilliant- very helpful!
@shawnmcmurtrey8090
2 жыл бұрын
Very good explanations!! Looking forward to watching more of your videos!
@zainabumarabdullahi9446
6 ай бұрын
No one can ever explain this better, love from Australia!
@mst63th
Жыл бұрын
Thanks, you make it easy to understand. Keep going.
@md.mohiuddinmasum3632
2 жыл бұрын
Simple and amazing explanation. This video deserves more views.
@TimoHromadka
Жыл бұрын
Great video, helped me disambiguate many concepts!
@KatharineME
Жыл бұрын
Glad it helped!
@spicesmiles
Жыл бұрын
Amazing! Succinct! Thank you!!!!
@LappingMaster
9 ай бұрын
GREAT VIDEO!!!!!!!!!
@franciscoromogaray3076
8 ай бұрын
Really clear, thanks!
@lolisimon2933
Жыл бұрын
Awesome video But Im not too sure about your explanation of genome coverage Your explanation for it sounded more like read depth
@KatharineME
Жыл бұрын
Right, I see your point. There are basically two concepts at hand which are both important for variant calling: one is percent of the genome that was sequenced, and the other is the number reads with a base call at a given nucleotide. For 30X depth sequencing, we want about 30 reads covering each nucleotide.
@markcuello5
Жыл бұрын
HELP
@KatharineME
Жыл бұрын
Any question is particular I can help with?
@e3.s.nro2tan75
Жыл бұрын
30 times coverage or 100 times coverage is better? Which is better on accuracy? Is 100x an over do or it is necessary to reduce the error margin?
@KatharineME
Жыл бұрын
Illumina sequencing does ~89% of base calls above Q30 (99.9% accurate). 30X means having ~30 base calls for each nucleotide. So 30X is usually all you need. 100X maybe used when high variation is expected, like in a tumor.
@carlloeber
Жыл бұрын
You are amazing..
@sanakhawer693
2 жыл бұрын
super helpful thank you so much.... please do a video on how to use different softwares
@KatharineME
Жыл бұрын
Hi! I have been working on some content for certain softwares, what software did you have in mind?
@saud319
2 жыл бұрын
So the company I tested with gave me these files but none of them is transferable to the famous ancestry data bases. Is there a way to convert them?
@chibi171
2 жыл бұрын
DNAgenics can convert whole genome files if that's what you mean. Into a RAW data file similar to 23andme and AncestryDNA etc. Which will allow you to upload your new results to third party sites.
@gerardmingarro6788
Жыл бұрын
excellent video!
@humarafique3093
8 ай бұрын
Superb👏
@جزائريهوآفتخر-ص9ث
Жыл бұрын
Thank you for your information, I have a question : in exam they ask always what's the difference between FastQ and Bam file, what is the best short answer for this question?
@hatchet646
Жыл бұрын
bam is aligned to the reference genome, fastq is not.
@KatharineME
Жыл бұрын
I would agree with that. The fastq file contains unordered reads. The bam file contains the same reads plus the location each maps to in the reference genome.
@mohamedesmailelsalahaty6050
2 жыл бұрын
Great go on
@dpchand
2 жыл бұрын
Awesome explanation... can you please tell how vcf file will look like if the segment from mother and father both have different nucleotide from that of reference?
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