Great work. Very clear steps you always offer in your tutorials that are very easy to follow. I also like that you attach further information about the useful links on your videos. Good job and keep it up.
Amazing thank you so much i was struggling from last 4 days. This helped a lot. Actually i am working with a hiv genome what next can we do with these results that we get at the end? How tu graphically visualise them? Can you please help me with my data? How can I contact you?
Do you have any tips on calling variants on say over 200 sequences at once? The example shown in this video covered a paired-end read of just 2 samples. Any comments?
Do you have any tips on calling variants on say over 200 sequences at once? The example shown in this video covered a paired-end read of just 2 samples. Any comments?
Nice tutorial! what would you do if you had more than one sample, say 2, and want to identify SNPs associated with each one of them? Would you do this process twice (One for each sample)?
I want to do all the analysis available on Quasi tools I.E aacoverage: builds an amino acid consensus and returns its coverage call aavr: call amino acid mutations for a BAM file and a supplied reference file call codonvar: call codon variants for a BAM file and a supplied reference file call ntvar: call nucleotide variants for a BAM file and a supplied reference file complexity: reports the complexity of a quasispecies using several measures consensus: generate a consensus sequence from a BAM file distance: measures the distance between quasispecies using angular cosine distance dnds: calculates the dn/ds value for each region in a bed file drmutations: identifies amino acid mutations hydra: identify HIV drug resistance mutations in an NGS dataset quality: perform quality control on FASTQ reads
Thanks for the tutorial. By using these steps, I realized that the "ID" column was missing (just dot symbols available for each varaints) in the final vcf file. How can we fix this problem?
It an excellent presentation, thank you very much Sir. When I run this command (bwa mem -t 8 ref/Agy99.fasta trimmed_R1.fastq.gz trimmed_R2.fast.gz > output.sam), I got this error=[E::bwa_idx_load_from_disk] fail to locate the index files. But when I run this code (bwa mem -t 8 ref/Agy.99.fasta trimmed_R1.fastq.gz trimmed_R2.fast.gz |samtools sort -o output.sorted.bam -) the error disappeared; what do you say about this error?
Thank you so much for this tutorial
You are amazing! This tutorial has saved us 2 weeks of work trying to learn variant calling. Thank you for such an amazing work.
I am happy to hear the video helped you. Let's keep it up.
Great work. Very clear steps you always offer in your tutorials that are very easy to follow. I also like that you attach further information about the useful links on your videos. Good job and keep it up.
Very helpful tutorial. You made variant calling very easy. Thank you so much.
Amazing thank you so much i was struggling from last 4 days. This helped a lot.
Actually i am working with a hiv genome what next can we do with these results that we get at the end? How tu graphically visualise them? Can you please help me with my data? How can I contact you?
Thank you so much for this tutorial viedo.
Do you have any tips on calling variants on say over 200 sequences at once? The example shown in this video covered a paired-end read of just 2 samples. Any comments?
Good stuff bro, thank you for sharing.
Download the Ebook and script from here: www.patreon.com/posts/variant-calling-77625038/
Do you have any tips on calling variants on say over 200 sequences at once? The example shown in this video covered a paired-end read of just 2 samples. Any comments?
@@ifyifemanima3972 For multiple samples you need to use a loop.
Nice tutorial! what would you do if you had more than one sample, say 2, and want to identify SNPs associated with each one of them? Would you do this process twice (One for each sample)?
Very helpful tutorial
I want to do all the analysis available on Quasi tools I.E
aacoverage: builds an amino acid consensus and returns its coverage
call aavr: call amino acid mutations for a BAM file and a supplied reference file
call codonvar: call codon variants for a BAM file and a supplied reference file
call ntvar: call nucleotide variants for a BAM file and a supplied reference file
complexity: reports the complexity of a quasispecies using several measures
consensus: generate a consensus sequence from a BAM file
distance: measures the distance between quasispecies using angular cosine distance
dnds: calculates the dn/ds value for each region in a bed file
drmutations: identifies amino acid mutations
hydra: identify HIV drug resistance mutations in an NGS dataset
quality: perform quality control on FASTQ reads
Can you tell me how to get a .bed file for a viral genome?
interested topic thank you
Thanks for the tutorial. By using these steps, I realized that the "ID" column was missing (just dot symbols available for each varaints) in the final vcf file. How can we fix this problem?
It think the ID column is used of the variant is known. This means you will have to do some annotation.
Thankssssssssssss 🤓
It an excellent presentation, thank you very much Sir. When I run this command (bwa mem -t 8 ref/Agy99.fasta trimmed_R1.fastq.gz trimmed_R2.fast.gz > output.sam), I got this error=[E::bwa_idx_load_from_disk] fail to locate the index files.
But when I run this code (bwa mem -t 8 ref/Agy.99.fasta trimmed_R1.fastq.gz trimmed_R2.fast.gz |samtools sort -o output.sorted.bam -) the error disappeared; what do you say about this error?
You have to generate the index first.
I suggest you watch the video again and follow all the steps.