How I perform Genome Mapping using BWA | Mapping any Reads to a Reference Genome | Paired-end Reads

[@mesfinworku6066]

Thank you for sharing

[@desaishailesh3527]

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]

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]

@@bioinformaticscoach thank you very much i will trt it

[@lakshmipraba4398]

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

[@Likitu264]

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

[@ZaenulMunnier]

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]

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

[@erindarruci1085]

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

[@kiplimosimon1429]

very informative. Thank you

[@alexandranikolaeva876]

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]

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]

@@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]

@@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]

@@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]

@@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.

[@dr.maqsoodahmad8572]

Very helpful Thanks

[@islamicmotivational_1786]

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

[@serychristianrenaud]

thank