Virus genome assembly and consensus sequence from reads

[@williamrosenbaum8882]

Can you do a igv video as a follow up? Thanks!

[@sanbomics]

I had planned to, but this video go so little love that I focused more on my transcriptomics content. I can place it back in the queue though, sure.

[@hyeokome]

@@sanbomics I'd also love to see IGV tutorials!!

[@Yueer-pe5ej]

Hi, I am confused that the "bwa mem" output is a .sam file, how can it be directly sorted by "samtools sort" option? Because the input of "samtools sort" is ought to be a bam file.

[@sanbomics]

samtools handles both bam and sam (hence why it is named SAMtools and not BAMtools). You can pipe the output of bwa directly into samtools no problem.

[@CilianMichael]

Thanks for this video. Is the sorted.bam indexed before using in samtools mpileup?

[@danieljairenriquezvera3340]

thanks for the video. I have a question, I have received three fastq files, I guess one is the index file, so may I omit it and use only R1 and R3? Thanks

[@sanbomics]

Don't use the index file. R3? there shouldn't be an R3. Only R1 and R2 if the sequences are paired

[@danieljairenriquezvera3340]

@@sanbomics I thought, may be R1 (1.8Gb) R3 (2.1 Gb), because R2 is the smallest one (432 MB). is it right?

[@ahmad.ramaddann]

Great video! Please do the IGV tutorial. Thanks.

[@sanbomics]

One day if i have time!

[@AnkeetKumar]

I loved your video. This has motivated me to learn bioinformatics. Do provide inputs if you have any for a beginner like me

[@sanbomics]

Wooo! Welcome to the club. 1) Learn basic linux Bash usage and how to use paths; 2) instead of starting with tutorials, come up with a feasible project/goal that is somewhat related to what you want to be doing eventually and learn as you go