Download all reads from a NCBI project.
module load sratoolkit edirect
esearch -db sra -query PRJNA40075 | efetch --format runinfo | cut -d ',' -f 1 | grep SRR | xargs fastq-dump --split-files
Or use prefetch for individual SRR* file
prefetch -v SRR5956435
fastq-dump --split-files SRR5956435
NCBI documents for downloading data: https://www.ncbi.nlm.nih.gov/books/NBK179288/
Perl one liner to extract sequences by their ID from a FASTA file
perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' ids.file fasta.file
perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file
SAM to sorted BAM
samtools view -@ 40 -u Wheat_E1_t1S_S8.sam | samtools sort -@ 40 -o Wheat_E1_t1S_S8.bam
CpG location on the genome
grep -v "^>" genome.fa | tr -d "\n" | tr -c "[GCgc]" "\n" | grep -v '^$' | grep -o -i 'CG' | wc -l
Extract all lines from a file which is present al list in gene.list
grep -Fw -f gene.list Tair10_GFF3_genes.gff
Get Multi Fasta Length
samtools faidx sample.fa
cut -f1-2 sample.fa.fai
Sum/average a column awk
awk -F',' '{sum+=$57;} END{print sum;}' file.txt
awk '{ sum += $2 } END { if (NR > 0) print sum / NR }' file.txt
| Selections | Commands |
|---|---|
| All Rows and All Columns | df[,] |
| First row and all columns | df[1,] |
| First two rows and all columns | df[1:2,] |
| First and third row and all columns | df[ c(1,3), ] |
| First Row and 2nd and third column | df[1, 2:3] |
| First, Second Row and second and third column | df[1:2, 2:3] |
| Just First Column with All rows | df[, 1] |
| First and Third Column with All rows- | df[,c(1,3)] |