jvineis / jgi-single-cell

A lab book for analysis of jgi single cell genomics

jgi-single-cell

A lab book for analysis of jgi single cell genomics

Download the files. I had to do this manually :( .. This must be fixed. either Haijk is going to fix it or I'm going to make my jgi-query script work. I moved the files from ~/Downloads to /Users/joevineis/Documents/BOWEN/jgi_single_cells/downloads. Then I unziped all files and decompressed the tar files

for i in `cat samples.txt `; do unzip $i'_FD_download.zip'; done

mkdir zip-directories-from-jgi
mv *.zip zip-directories-from-jgi/
ls *Raw/IMG\ Data/ | grep .gz > tar-files.txt
for i in `cat tar-files.txt`; do tar -zxvf *Raw/IMG\ Data/$i; done

Collect all of the fna files an generate contigs.dbs

 mkdir SAG-genomes-fa-files
 mv 27*/*.fna SAG-genomes-fa-files/
 
 ls *.fna | sed 's/\.fna//g' > samples.txt

 for i in `cat samples.txt `; do anvi-script-reformat-fasta $i'.fna' -l 0 --simplify-names -o $i'-simpleids.fna'; done
 for i in `cat samples.txt `; do anvi-gen-contigs-database -f $i'-simpleids.fna' -n $i'-single-cell' -L 5000 -o $i'-contigs.db'; done

Add some important hmm gene calls to the db and ncbi cogs.

for i in *contigs.db; do anvi-run-hmms -c $i; done
for i in `cat samples.txt`; do anvi-run-ncbi-cogs -c $i'-contigs.db' -T 10 --sensitive; done

For phylogenetic analysis.

1. explore the completeness etc for each SAG

 working from here: /Users/joevineis/Documents/BOWEN/jgi_single_cells/downloads/SAG-genomes-fa-files
 anvi-display-contigs-stats *.db

 anvi-get-sequences-for-hmm-hits --external-genomes external-genomes.txt \
                            -o concatenated-proteins.fa \
                            --hmm-source Campbell_et_al \
                            --gene-names Ribosom_S12_S23, Ribosomal_L1, Ribosomal_L10, Ribosomal_L11, Ribosomal_L11_N, Ribosomal_L12, Ribosomal_L13, Ribosomal_L14, Ribosomal_L16, Ribosomal_L17, Ribosomal_L18e, Ribosomal_L18p, Ribosomal_L19, Ribosomal_L2, Ribosomal_L20, Ribosomal_L21p, Ribosomal_L22, Ribosomal_L23, Ribosomal_L27, Ribosomal_L28, Ribosomal_L29, Ribosomal_L2_C, Ribosomal_L3, Ribosomal_L32p, Ribosomal_L35p, Ribosomal_L4, Ribosomal_L5, Ribosomal_L5_C, Ribosomal_L6, Ribosomal_L9_C, Ribosomal_L9_N, Ribosomal_S10, Ribosomal_S11, Ribosomal_S13, Ribosomal_S15, Ribosomal_S16, Ribosomal_S17, Ribosomal_S18, Ribosomal_S19, Ribosomal_S2, Ribosomal_S20p, Ribosomal_S3_C, Ribosomal_S4, Ribosomal_S5, Ribosomal_S5_C, Ribosomal_S6, Ribosomal_S7, Ribosomal_S8, Ribosomal_S9 \
                            --return-best-hit \
                            --get-aa-sequences \
                            --concatenate