Some questions of the pipeline

[tianxiahuihui]

After reading the documents, I have other questions in main.sh.
1.What is the difference about CARD gene_homology and CARD gene_variant. The two same command only make same results.
2.What to do next when we get CARD_gene.bam file.
3.Author also need to warn the user to use the latest samtools version.
4.The command "samtools view -bS $OUT_DIR/$sra.CARD_gene.sam | samtools sort - $OUT_DIR/$sra.CARD_gene.bam" need to be changed "samtools view -bS $OUT_DIR/$sra.CARD_gene.sam | samtools sort -o $OUT_DIR/$sra.CARD_gene.bam"

[stevetsa]

Thank you for your interest in this project. I have updated the documentation in my fork.

1. Please refer to the CARD database for detailed description of their data
2. In the updated version, we made some suggestions about possible next steps, which is beyond the scope of this project.
   3&4) Yes and a Docker container is available for this reason.

[tianxiahuihui]

I am sorry. I do not understand the possible next steps. Docker is just a Container which have some software, but what I need is command sets. How to convert the bam file to output format file and dot plot? Could you provide the example which you deal with ERR1600439 and ERR1600437 data?