Bioinfo concepts

gunzip -c x.txt.gz >x.txt

Download atom-amd64.deb from the Atom releases page . Run sudo dpkg --install atom-amd64.deb on the downloaded package. Launch Atom using the installed atom command. goto setting in atom install package language-perl6fe

Open the terminal. (CTRL + ALT + T) Look for the USB drive you want to format, by running: $ df Unmount drive using the syntax below: $ sudo umount /dev/sdc1( pendrive drive) Now run this command to format drive to fat32: sudo mkfs.vfat -n 'Ubuntu' -I /dev/sdc1( pendrive drive)

install bamtools sudo apt-get install cmake wget http://clavius.bc.edu/~erik/freebayes/freebayes-5d5b8ac0.tar.gz tar xzvf freebayes-5d5b8ac0.tar.gz cd freebayes make Now that freebayes is built, we can run it: bin/freebayes # default summary bin/freebayes -h # verbose help text, summary of options

Makefile:39: recipe for target '../bamtools/lib/libbamtools.a' failed make[1]: *** [../bamtools/lib/libbamtools.a] Error 127 install bamtools sudo apt-get install cmake wget http://clavius.bc.edu/~erik/freebayes/freebayes-5d5b8ac0.tar.gz tar xzvf freebayes-5d5b8ac0.tar.gz cd freebayes make

COSMIC - Registration  download  WinSCP       Host name:     sftp-cancer.sanger.ac.uk       Protocol:      sftp       Port:          22       Username:      Your email address       Password:      Your password Once logged in you will need to download the file from this location /files/grch38/cosmic/v76/    

Rakudo: Is a compiler for Perl 6. Rakudobrew: Is an installation manager for Rakudo. Panda: Is a Perl 6 module installer. Rakudo Star: Is a bundle that includes Rakudo, Panda, a collection of Perl 6 modules, and documentation. Install Rakudobrew: sudo apt-get install build-essential git git clone https://github.com/tadzik/rakudobrew ~/.rakudobrew echo 'export PATH=~/.rakudobrew/bin:$PATH' >> ~/.bashrc source ~/.bashrc Install Rakudo: Type the following command in the terminal rakudobrew build moar Install Panda: Type the following command in the terminal rakudobrew build panda Restart computer

 ~/Platypus/Platypus_0.8.1 $ ./buildPlatypus.sh Building Platypus running build running build_py running build running build_py running build running build_py running build running build_py running build running build_py running build running build_py running build running build_py running build running build_py running build running build_ext building 'ctabix' extension x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/usr/include/python2.7 -c ctabix.c -o build/temp.linux-x86_64-2.7/ ctabix.o ctabix.c:8:22: fatal error: pyconfig.h: No such file or directory  #include "pyconfig.h"                       ^ compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 then install  sudo rm /var/lib/dpkg/lock sudo dpkg --configure -a sudo apt-get install p...

1 ) open  Bio::DB::Sam and download or sudo perl -MCPAN -e shell install  Bio::DB::Sam 2) if it give you this line "Please enter the location of the bam.h and compiled libbam.a files:" then enter your samtools path like   " /home/anop/Desktop/igib/project/ samtools-1.3.1 /"  which is hold bam.h and  libbam.a

Exception in thread "main" net.sf.samtools.SAMFormatException: SAM validation error: ERROR: Record 630636, Read name HWI-H212:69:C0NR3ACXX:1:1212:10100:13262, bin field of BAM record does not equal value computed based on alignment start and end, and length of sequence to which read is aligned at net.sf.samtools.SAMUtils.processValidationErrors(SAMUtils.java:448) at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:541) at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:522) at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:481) at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:672) at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:650) at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:397) at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:161) at net.sf.picard.cmdline.CommandLi...

dpkg: error processing package libpcre3:amd64 (--configure):  package libpcre3:amd64 2:8.35-7.1ubuntu1.4 cannot be configured because libpcre3:i386 is at a different version (2:8.35-7.1ubuntu1.3) Errors were encountered while processing:  libpcre3:amd64 E: Sub-process /usr/bin/dpkg returned an error code (1) install both ..... libpcre3-dev_8.35-7.1ubuntu1.3_amd64.deb libpcre3-dev_8.35-7.1ubuntu1.3_i386.deb and install all  Depended   Package ............ https://launchpad.net/ubuntu/wily/amd64/libpcre3-dev/2:8.35-7.1ubuntu1.3

when Error in Trimmomatic command line /usr/local/bin/trimmomatic: line 1: $'PK\003\004': command not found /usr/local/bin/trimmomatic: line 2: $'\bi\203uH': command not found /usr/local/bin/trimmomatic: line 3: syntax error near unexpected token `$'\a\217\245\234D\312\017\265\026\234\311{\234T\315.\204\024\266ת\353\2179\343\354\003PK\003\004'' /usr/local/bin/trimmomatic: line 3:h�uH��\ �� META-INF/MANIFEST.MFM�=� w � ��GSS�V;7.ƕ�ҧ �h��{�����F��N� ��R< ���>��~A�$��- U�ِ +������ �i �}M���i@�F���; ������z C�K�X]�L�=g#�(�D� ��{�T�.� �ת��� PK ' then simple  you can adding "java -jar" like this  java -jar trimmomatic SE -threads 4 -phred33 input output AVGQUAL:20 SLIDINGWINDOW:5:20 MINLEN:50`;