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Anna Battenhouse

Anna Battenhouse

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Code Block
languagebash
titleStart an idev session
idev -m 180 -N 1 -A OTH21164 -r CoreNGS -Tue   
  # or -A TRA23004 
# -or-
idev -m 120 -N 1 -A OTH21164 -p development   # or -A TRA23004

Data staging

Set ourselves up to process some yeast data data in $SCRATCH, using some of best practices for organizing our workflow.

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Line 3 always starts with '+'  (it can optionally include a sequence descriptionIt can be populated by downstream tools)

Line 4 is a string of Ascii-encoded base quality scores, one character per base in the sequence.

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Code Block
languagebash
titlegzip, gunzip exercise
# if the $CORENGS environment variable is not defined
export CORENGS=/work/projects/BioITeam/projects/courses/Core_NGS_Tools

# make sure you're in your $SCRATCH/core_ngs/fastq_prep directory
cd $SCRATCH/core_ngs/fastq_prep

# Copy over a small, uncompressed fastq file
cp $CORENGS/misc/small.fq .

# How many lines does it have?
wc -l small.fq

# check the size, then compress it in-place
ls -lh small*
gzip small.fq

# check the compressed file size
ls -lh small*

# uncompress it again
gunzip small.fq.gz
ls -lh small*

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Code Block
languagebash
titleUsing the head command
# shows 1st 10 lines
head small.fq

# shows the first 2 lines
head -n 2 small.fq
head -2 small.fq

# shows 1st 100 lines -- might want to pipe this to more to see a bit at a time
head -100 small.fq | more

So what if you want to see line numbers on your head (or tail) output? Neither command seems to have an option to do this.

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