Problems Input

[diaz13]

hi

I want to use your pipeline. But I do not know how to get the right input bam. Because there are several ways with the bam files.
So I had a strategies to show by the following command lines:
1- bwa index 1.fasta
2- bwa mem 1.fasta 1_S1_L001_R1_001.fastq 1_S1_L001_R2_001.fastq > 1.bam
3- python3.6 panISa.py 1.bam -o 1.txt
4- python3.6 ISFinder_search.py -o 1 -i 80 -a 60 1.txt

You think it's good as input to find the sequences of insertions???
Are there any errors in my command lines ???
Where can I find the ISinfo file for Francisella's example species ??? To do the IS validation.

Thanks in advance for your help

[bvalot]

Hi,

Normally, panisa used any bam file, but be careful because bwa output by default a sam file.
2- bwa mem 1.fasta 1_S1_L001_R1_001.fastq 1_S1_L001_R2_001.fastq | samtools view -Sb - -o - > 1.bam

For run panisa, the bam file input must be at the end normally, as it is a positional argument
3- python3.6 panISa.py -o 1.txt 1.bam

I don't understand your question about ISinfo file for Francisella's example species?

Benoit

[diaz13]

Thanks you @bvalot

My last question concerning a validation of IS. I run the following command
python3.6 validate.py -o 1.tab 1.fasta 1.txt
I see in your example this file (/home/user/Tools/panISa-master/validate/example/ISinfo/Escherichia_coli)
I asked where does this file (/home/user/Tools/panISa-master/validate/example/ISinfo/Escherichia_coli) come from?

thanks

[bvalot]

Ok,

This files were extracted from ISFinder database to performed in sillico validation of our tools. You can have a more complete list here:
https://www-is.biotoul.fr/

[diaz13]

ok
I understand.
thanks you.