Address of the bookmark: http://readiab.org/

Foreign nationals intending to have certification are eligible to appear for BINC examination.
Minimum qualification includes a degree from a recognized university/institute in the areas listed in FAQ.
Formal training in the area of Bioinformatics is not a prerequisite.
Note that the foreign students will only be certified by DBT and are not eligible for the cash award as well as junior research fellowship.

Address of the bookmark: http://binc.scisjnu.ernet.in/

Courses

Old courses (2012-2014)

Metagenomics Workshop

2015 November - Uppsala
2016 November - Uppsala
2017 November - Uppsala

Introduction to Bioinformatics Using NGS Data

2015 February - Uppsala 
2015 May - Gothenburg
2015 September - Uppsala
2015 November - Lund
2016 January - Uppsala
2016 April - Linköping
2016 September - Uppsala
2016 November - Umeå
2017 January - Uppsala
2017 May - Gothenburg
2017 September - Lund
2017 November - Uppsala
2018 February - Uppsala

Introduction to Genome Annotation

2015 April - Uppsala
2016 April - Uppsala
2017 April - Uppsala
2018 May - Uppsala

De Novo Genome Assembly

2016 November - Uppsala
2017 November - Uppsala

RNA-seq course

2015 October - Uppsala
2016 April - Uppsala
2016 October - Uppsala
2017 March - Uppsala
2017 November - Uppsala
RNAseq tutorials

R Programming Foundations for Life Scientists

2016 November - Uppsala
2017 Mars - Uppsala

Single cell RNA sequencing analysis

2017 October - Uppsala

Address of the bookmark: https://scilifelab.github.io/courses/

Address of the bookmark: http://www.rdatamining.com/

Awk is a programming language that is specifically designed for quickly manipulating space delimited data. Although you can achieve all its functionality with Perl, awk is simpler in many practical cases.

Why awk? You can replace a pipeline of 'stuff | grep | sed | cut...' with a single call to awk. For a simple script, most of the timelag is in loading these apps into memory, and it's much faster to do it all with one. This is ideal for something like an openbox pipe menu where you want to generate something on the fly. You can use awk to make a neat one-liner for some quick job in the terminal, or build an awk section into a shell script. You can find a lot of online tutorials, but here I will only show a few examples which cover most of bioinformatician daily uses of awk.

choose rows where column 3 is larger than column 5:

awk '$3>$5' input.txt > output.txt

extract column 2,4,5:

awk '{print $2,$4,$5}' input.txt > output.txt

awk 'BEGIN{OFS="\t"}{print $2,$4,$5}' input.txt

show rows between 20th and 80th:

awk 'NR>=20&&NR<=80' input.txt > output.txt

calculate the average of column 2:

awk '{x+=$2}END{print x/NR}' input.txt

regex (egrep):

awk '/^test[0-9]+/' input.txt

calculate the sum of column 2 and 3 and put it at the end of a row or replace the first column:

awk '{print $0,$2+$3}' input.txt

awk '{$1=$2+$3;print}' input.txt

join two files on column 1:

awk 'BEGIN{while((getline<"file1.txt")>0)l[$1]=$0}$1 in l{print $0"\t"l[$1]}' file2.txt > output.txt

count number of occurrence of column 2 (uniq -c):

awk '{l[$2]++}END{for (x in l) print x,l[x]}' input.txt

apply "uniq" on column 2, only printing the first occurrence (uniq):

awk '!($2 in l){print;l[$2]=1}' input.txt

count different words (wc):

awk '{for(i=1;i!=NF;++i)c[$i]++}END{for (x in c) print x,c[x]}' input.txt

deal with simple CSV:

awk -F, '{print $1,$2}'

substitution (sed is simpler in this case):

awk '{sub(/test/, "no", $0);print}' input.txt

OK now here's where to read this stuff properly explained. roll

Two thorough tutorials:

http://www.gnu.org/software/gawk/manual/gawk.html

http://www.grymoire.com/Unix/Awk.html

A famous list of useful one-liners - though they're short, many are quite tricky:

http://www.pement.org/awk/awk1line.txt

And some nice explanations of those one-liners. After reading this you'll have a pretty good grasp!

http://www.catonmat.net/blog/awk-one-li … -part-one/

http://www.catonmat.net/blog/ten-awk-ti … -pitfalls/

(Indian Council of Medical Research )
Jehangir Merwanji Street, Parel, Mumbai 400 012

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