Schumer lab: Commonly used programs

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Example usage of commonly used programs

Programs to overlap files & more

bedtools is an incredibly useful program for overlap files of many common format types. Check out the bedtools documentation here [[1]]

Here are some examples we commonly use:

1) overlap a bed file with another bed file, or a large number of other possible formats (gff, gtf, vcf, etc):

/home/groups/schumer/shared_bin/bedtools2/bin/intersectBed -a infile1.bed -b infile2.vcf -wo > outfile.bed

see bedtools documentation for the many options in overlapping files [[2]]

2) calculate coverage in a particular region of a bam file:

/home/groups/schumer/shared_bin/bedtools2/bin/multiBamCov -bams file.bam -bed region_of_interest.bed -q 30 > results

3) convert a bam file to a fastq file:

/home/groups/schumer/shared_bin/bedtools2/bin/bamToFastq -i file.bam -fq file.fq

PLINK: the genomics Swiss army knife

If you want to calculate a basic pop-gen statistic or analysis, chances are plink can do it. Here is a small subset of the things plink can do, see the plink homepage for details [[3]]

Determine pairwise LD between SNPs or AIMs:

/home/groups/schumer/shared_bin/plink infile-name-stem --ld-window-kb 5000 --ld-window 20000 --r2 --hardy --hwe 0.001 --out outfil-name-stem-ld_decay --ld-window-r2 0 --allow-extra-chr

Make sure to check out the command line parameters. If you want to calculate r or D instead, replace the r2 flag

plink can convert between a large number of file formats, perform HWE filtering, LD pruning, identify mendelian errors, and more

Running blast from the command line

BLAST is a powerful algorithm for searching for alignments between sequences of varying levels of divergence. It is most efficient for search for one of a few sequences in a large database (i.e. a genome).

On sherlock, load the blast modules:

module load biology module load ncbi-blast+

Format your database for blast search:

makeblastdb -in genome.fa -dbtype nucl

Run your blast job:

blastn -db genome.fa -query my_gene.fa -task blastn -out my_gene_blast_results -evalue 1e-20 -outfmt 6

Larger e-values will result in more alignments

The unnamed columns in the output file are as follows:

query_sequence reference_sequence percent_identity alignment_length mismatches gaps query_start query_end reference_start reference_end e-value bit_score

Aligning fasta sequences

Aligning long sequences

For aligning long (i.e. ~chromosome length) sequences, mummer [[4]] works great! Remember to read the documentation and tune your parameters based on divergence between the sequences your aligning.

1) align sequences

/home/groups/schumer/shared_bin/mummer-4.0.0rc1/nucmer fasta_chr1_species1.fa fasta_chr1_species2.fa -l 100 -c 200 --prefix=chr-name-prefix

2) mark and filter alignments

/home/groups/schumer/shared_bin/mummer-4.0.0rc1/delta-filter -m >

3) plot results

/home/groups/schumer/shared_bin/mummer-4.0.0rc1/mummerplot -large -layout --png -p chr-name-prefix

if mummerplot in step 3 doesn't work (, you can always plot the *.delta.m file in R using this workflow (

Aligning shorter sequences, genes or proteins

For aligning short sequences, particularly genes and proteins, clustal omega is very useful. Note: clustal omega will not work if the two sequences you're aligning aren't the same orientation. The input file is a single fasta containing all of the sequences you would like to align.

/home/groups/schumer/shared_bin/clustalo-1.2.4-Ubuntu-x86_64 -i infile_gene1_allspecies.fa -o clustal_align_gene1_allspecies.aln --outfmt=clustal -v --force

Programs to adapter and quality trim fastq files

Trimgalore is a great program for trimming adapter sequences from your reads.

To trim single-end reads:

/home/groups/schumer/shared_bin/TrimGalore/trim_galore --path_to_cutadapt /home/groups/schumer/shared_bin/cutadapt --phred33 --quality 30 -e 0.001 --stringency 1 --length 32 SE_read.fq.gz

To trim paired-end reads:

/home/groups/schumer/shared_bin/TrimGalore/trim_galore --path_to_cutadapt /home/groups/schumer/shared_bin/cutadapt --phred33 --quality 30 -e 0.001 --stringency 1 --length 32 --paired -retain_unpaired PE_read1.fq.gz PE_read2.fq.gz

Programs to map reads and call variants

For genomic data, see Mapping and variant calling

For RNAseq data, see Mapping and RNA quantification

Programs to build phylogenies

One of the most commonly use programs for phylogenetic reconstruction in the lab is RAxML

The RAxML program can be found here:


1) Preparing fasta files:

RAxML requires as input a multi-fasta alignment file. RAxML does not accommodate polymorphic basepairs so either mask them:

perl -pi -e 's/[RYSWKM]/N/g' myfasta.fa

or use a coin flip approach to convert them to non-IUPAC codes:

perl infile.fa > outfile_coinflip.fa

2) Optionally, trim aligned fasta files to variable sites to run RAxML quickly:

module load biology py-biopython

python -v myfasta.fa -o myvariablefa.fa

3) Run RAxML

See the RAxML documentation for specific applications (i.e. for coding sequences). For an alignment that is mainly non-coding, here is a commonly used command to generate a maximum likelihood tree with 100 bootstraps:

/home/groups/schumer/shared_bin/raxmlHPC-PTHREADS -f a -m GTRGAMMA -p 12345 -x 12345 -s myvariablefa.fa -# 100 -n myresults_name

You can add multi threading with the -T option but make sure your number of requested cpus matches or it will run much more slowly than without multi threading

You can visualize your results with desktop applications like FigTree

General use programs