This Scientifically crazy life

Hola!

Copying left over files and merging is really easy via GUI (graphical user interface) but when it comes to command line, transferring big files or copying fast or usage of script, I always lacked a tool to resume the copy, when it stops or fails in between.

The tool in 'rsync', It was developed in 1996 but still we are ignorant about it.

Quickly using rsync to resume copy:

rsync -a - -progress source/folder/ destination

* Note the slashes, if you want to copy left over items from one folder to another, the folder should be present in the destination dir with the same name as in the source. So, in this case, a folder named 'folder' is present in the destination dir. and the copy will resume with left over files.

'- - progress' is really nice, and will tell you what the tool is copying at the moment.

Have Fun

Leute!!

Suppose you have a list of 20 dataframes, each of data frame has 10 columns but different rows. You want to know the length of rows in each dataframe without using loop in a single line.

sapply(x,function(y)length(y[[1]]))

where x is a list

If you are after a specific column, just replace the number [[1]] with it.

Cheers

Hola people!

Quick tutorial on how to convert bam file to bedGraph (different from bed files) for displaying them into UCSC browser. We will convert them to bigwig (bw), which are more portable, encrypted and less space consuming data formats.

Step 1: using a combination of 'samtools' and 'bedtools' and ofcourse 'shell pipe'

samtools view -b file.bam | genomeCoverageBed -ibam stdin -bg -g genomeIndex/mm9.chrom > file.bedGraph &

input file = file.bam; output = file.bedGraph

genomeIndex = mm9.chrom (to get the genome index, which a text file containing the mouse genome size per chromosome, use fetchChromSizes, get it from UCSC ftp http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes)

Step2 : sort obtained bedGraph file chromosome wise using sort

sort -k1,1 -k2,2n file.bedGraph > file.bedGraph.sorted

Step 2: converting bedGraph to bigwig

using  bedGraphToBigWig utility from UCSC tools (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig)

bedGraphToBigWig file.bedGraph.sorted genomeIndex/mm9.chrom file.bw

I will make another post, how to use 'bw' (bigwig) files for viewing them on server using a https link and sharing a url.

Any problems, please comment, I will try to answer.

Cheers

Sukhdeep Singh

Hey, using sed is awesome if you know how to use it.

 sed -i 's/yo/yeah/g' b 

where b is the name of file from where the input is taken and where it gonna store it back and yo is being searched to be replaced with yeah.

Have fun with 'sed'

Cheers