Thanks Simon! I've found your lectures very informative and helpful. I've been catching up. I have a question about this lecture. Do we need to cut the adaptors before running a bowtie2 mapping. Will the adapters affect the accuracy of the mapping? Thank you!
Hi Hui, Sorry for jumping to answer! Yes you have to remove the adapter from your read because it's non-biological sequence. It's important also to remove bad read with low phred score. many tools dose this for you i did test catadapt & trimmomatic both is good but in my opinion trimmomatic is much easier
Hi Simon, I have a question to ask, do the reads and the index have to be in the same directory as we perform bowtie2 alignment because I dont have to create the index as the reference genome was already downloaded on the university cluster, but it wont allow me to move the reference genome to my own directory without the permission. This is the command I used: bowtie2 -q dm6 -1 SRR3845160_1.fastq -2 SRR3845160_2.fastq -S SRR3845160.sam, however, the cluster said that it has no index, query or output file specified. Do you know what is going wrong with the command?
( "human" does not exist or is not a Bowtie 2 index ) instead of ecoli_k12 i gave name human and my files formed were human.1.ebwt ,can you please help me with this error
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really nice sessions thank you.!
Very Very Very nice tutorial
Thanks simon, bowtie2 can accept as input a file which contain a lot of reference sequences? and more than one read-containing file?
What's the difference between using Bowtie vs a recruitment plot by blast?
Thanks Simon! I've found your lectures very informative and helpful. I've been catching up. I have a question about this lecture. Do we need to cut the adaptors before running a bowtie2 mapping. Will the adapters affect the accuracy of the mapping? Thank you!
Hi Hui,
Sorry for jumping to answer!
Yes you have to remove the adapter from your read because it's non-biological sequence. It's important also to remove bad read with low phred score. many tools dose this for you i did test catadapt & trimmomatic both is good but in my opinion trimmomatic is much easier
@@abdullahmohammed9347 Thanks for your answer! It's very helpful!
Muchas gracias!!
Hi Simon, I have a question to ask, do the reads and the index have to be in the same directory as we perform bowtie2 alignment because I dont have to create the index as the reference genome was already downloaded on the university cluster, but it wont allow me to move the reference genome to my own directory without the permission. This is the command I used: bowtie2 -q dm6 -1 SRR3845160_1.fastq -2 SRR3845160_2.fastq -S SRR3845160.sam, however, the cluster said that it has no index, query or output file specified. Do you know what is going wrong with the command?
Thank you it was very helpful
hello, could you tell me from where I get gcf.........fna file for mapping in bowtie2
Where is the same channel for PC users. I swear once I can afford a mac I will get one.
You can use virtual box to follow this tutorial along
( "human" does not exist or is not a Bowtie 2 index
) instead of ecoli_k12 i gave name human and my files formed were human.1.ebwt ,can you please help me with this error
I mean GCF_000005845.2_ASM584V2-genomic.fna