It's really helpful for my project. Thanks a lot 🙏

Very helpful Thanks

very informative. Thank you

thank

Hello the vedio is very helpful Can you share vedio on same concept but using python That will be very grateful Thanks

this is super and thanks for making it, but the question I was having after alignment in case you want to remove the non-aligned sequence (possible to reduce the size or even no use of data of non-alignment), how only we can keep aligned data?

@bioinformaticscoach

Жыл бұрын

you can use samtools to filter the alignment records.eg. select reads with mapped mate pairs, reads with a particular mapping quality,etc. Alternatively you can book a session with me and we can go through the steps.

@desaishailesh3527

Жыл бұрын

@@bioinformaticscoach thank you very much i will trt it

This is super helpful, thank you! I am wondering what are the benefits of converting to BAM besides the fact that it is a smaller file. Do you lose any information when you convert?

@bioinformaticscoach

Жыл бұрын

You don't lose any information at all. But I recommend you use the bam files especially if dealing with lots of samples. Smaller files also mean less computational constraint

@alexandranikolaeva876

Жыл бұрын

@@bioinformaticscoach Awesome, thank you! Your videos are super helpful! I am using BAM files in the downstream application to check the ploidy of my samples, and this is the most straightforward explanation on the alignment that I was able to find so far!

@bioinformaticscoach

Жыл бұрын

@@alexandranikolaeva876 It is also important to perform filtering of the alignment records in the bam files. I working on a tutorial on that. This will be released next month. You can use tools like samtools and bamtools.

@alexandranikolaeva876

Жыл бұрын

@@bioinformaticscoach That's really awesome, thanks! One more question - in bwa mem command, how much does the number of threads matter (8)? My file has been running for 2 hours now, but I have a very big genome (27 gb). Do you think I can decrease that number without loss of information?

@bioinformaticscoach

Жыл бұрын

@@alexandranikolaeva876 Genome mapping is computationally expensive. So you need a high end PC or better still a Computer Server. You can then increase the number of threads to make BWA run faster.

It really helpful I got 34 file s of R1 Illumina reads and 34 files of R2 Illumina reads Since it is not easy to write down them all in a command just like bwa mem -t 8 .... Could you help me to write a script just to merge them all?

@bioinformaticscoach

11 ай бұрын

Yes. That can be done. You can book a session and I will work on it.

@erindarruci1085

Ай бұрын

Hi, did you perform any trimming , or are you using the raw reads? Thank you!!

What is the best software to perform alignment of a file that contains many sequences? Im gonna be working with data from an ilumina NGS sequencing panel, is about 100 human genes, only coding regions and 20bp from flanking introns