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In the section How to visualize genomic variation (What would realistic and good data look like?) it says that the script simulate-experimental-data.sh will generate a file called results.bam. It actually generates a file called align.bam.
Just a small follow up on the issue:
The text after the fixed link in Variant effect prediction is not correct as it states that the script needs to be edited to modify the accession number. The accession number is given as a parameter on the command line so no editing is needed.
In addition, for running the annotation after the script the command snpEff ebola_zaire samples.vcf > annotated.vcf is suggested. The script will produce a vcf file for each run and one for all runs combined: SRR19729[17,18,19,20,21].vcf and combined.vcf. None is called samples.vcf. It is quite obvious what is meant but may be confusing for a newbie trying to learn.
As reported in:
https://www.biostars.org/p/225812/#242326
In the section How to visualize genomic variation (What would realistic and good data look like?) it says that the script simulate-experimental-data.sh will generate a file called results.bam. It actually generates a file called align.bam.
In the section Variant effect prediction (How do I use snpEff?) the link http://data.biostarhandbook.com/variant/find-ebola-variants.sh results in a file not found error. Please check, thanks.
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