BOL: Related items

Postdoctoral scientist genome analytics/ genome bioinformatics (m/f/*)

Sun, 16 Feb 2020 02:57:40 -0600

https://www.uksh.de/jobs/Stellenangebote-nr-20190570-p-8.html
Your profile:
Degree in bioinformatics, biostatistics, or equivalent
Experience in the processing and analysis of large-scale genomics data using compute clusters / high-performance computing
Strong competence in working in Unix/Linux environments (shell)
Strong programming skills (in particular: Python, R, Perl)
Experience with using git and snakemake
Fluent English language skills, both spoken and written
Strong communication skills and motivation to work in a young, interdisciplinary, dynamic team

Additional Information:

If you have any questions about scientific aspects of this position, please contact Prof. Lars Bertram, head of LIGA (lars.bertram@uni-luebeck.de).

Please contact Ms. Anna Wolbert for further questions about administrative details (recruiting@uksh.de).

Weitere Informationen erhalten Sie auch unter www.uksh.de/karriere.

Wir freuen uns auf Ihre Bewerbung bis zum 15.03.2020 unter Angabe unserer Ausschreibungsnummer 20190570.119.CL.

Postdoc Position in Computational Biology

Fri, 14 Mar 2014 01:38:49 -0500

The Computational Biology Group of Interdisciplinary Center for
Clinical Research (IZKF) Aachen, RWTH Aachen University Hospital,
Aachen, invites applicants for PhD candidate or postdoctoral position
in computational biology in one of the following topics:

1) Statistical machine learning methods for the analysis of medical
epigenomics data.

2) Sequence analysis algorithms for detection of RNA-DNA interactions.

Applicants should hold a M.Sc . or PhD in Computer Science or related
areas. Experience in the analysis of biological sequences, gene
expression and gene regulation is desirable. The candidate should have
solid programming skills (C, Python and/or R) and acquaintance with
Linux. Experience with high performance computing is a plus. The
working language of the group is English.

The position is based on the German TV-L 13 salary scale, including
all German social benefits (health insurance and pension scheme). The
expected starting date is September 2014. Interested candidates should
send a CV, statement of research interests and the names of three
references to jobs@costalab.org.

More at http://costalab.org/wp/phd-and-postdoc-position-in-computational-biology/

Choosing the Right NGS Sequencing Instrument for Your Study

Neel — Wed, 15 Jun 2022 00:37:29 -0500

The right sequencing instrument for your study depends on your project goal. Setting aside turnaround time and price, it essentially comes down to the numbers of reads and read length you need for your experiment. Below, we've described and compared metrics for each of the instruments available. If you’re new to high-throughput sequencing and have questions about how you should design your sequencing run, fill out our free consultation form and we'll get in touch with you to help.

More at https://genohub.com/ngs-instrument-guide/

Address of the bookmark: https://genohub.com/ngs-instrument-guide/

BioGeek Fun

Jit — Sun, 16 Mar 2014 06:33:31 -0500

1. A futuristic computational biology student was told to write "It is in my gene!!!" on the board 100 times as a punishment. here's his response -

use warnings;
for ($count=1; $count <=100; $count++) { print "It is in my gene!!!";}

I guess, he is gonna to be a real biogeek. Nice try though. Smart kid.

2. In some perl script I found this
. . . . . .
. . . . . .
# It works for me, only God understood how it is working
while (/(<\/[^>]+>)|(<[^>]+>)|(<[^>]+>)$|([^><]+)/go) {
            $startGene=$1;
            $beginChromosome=$2;

. . . . . .
.. . . . . .
}

3. One more interesting message in Perl found …. It will must tickle you bone :)
open(my $fh, "<", "gene.txt") or kill " Me if you think this is a mistake :$!";

4. From the Perl

while () { # "The Mothership Connection is here!"
print “$_\n”; # Printing the offspring :)

5. Perl message
if ($1) { print “Just found a the error in chromosome !!!, yahoo…”; else { “That is not error, but mutation you moron!”;

6. One genome database curator walk in wine bar asked the bartender:
CREATE TABLE gene IF NOT EXISTS SexOnTheBeach;

Common steps for reads mapping !

BioStar — Thu, 09 Mar 2023 02:48:02 -0600

Mapping reads to a reference genome is an essential step in many types of genomic analysis, such as variant calling and gene expression analysis. Here are some general steps to follow for mapping reads to a genome:

Choose a read mapper: There are many read mappers available, such as BWA, Bowtie, and HISAT2. Choose a mapper that is appropriate for your type of data and research question.
Index the reference genome: Before mapping reads, the reference genome needs to be indexed. This involves creating an index of the genome sequence that allows the mapper to quickly find matches to the reads. Most mappers have their own indexing tools.
Prepare the read data: The reads should be in a format that is compatible with the mapper. Most mappers accept FASTQ or BAM files. Depending on the quality of the data, it may need to be filtered or trimmed before mapping.
Run the mapper: The mapper is run with the command-line interface or using a graphical user interface. The specific command depends on the mapper being used, but typically involves specifying the input data, reference genome, and output file format.
Evaluate the mapping results: After the mapping is complete, the results should be evaluated. This includes assessing the quality of the mapping, such as the mapping rate, the number of mapped reads, and the mapping quality score.
Post-processing: Depending on the analysis being performed, post-processing of the mapped reads may be necessary. This can include filtering reads based on quality, removing duplicate reads, and calling variants.

Overall, mapping reads to a reference genome is a complex process that requires careful consideration of the type of data, the research question, and the specific mapper being used.

Jarvis’ laboratory

Tue, 18 Mar 2014 18:53:47 -0500

Dr. Jarvis’ laboratory studies the neurobiology of vocal communication. We want to know how the brain generates, perceives, and learns behavior. We use vocal communication as a model behavior. Emphasis is placed on the molecular pathways involved in the perception and production of learned vocalizations. We use an integrative approach that combines behavioral, anatomical, electrophysiological, and molecular biological techniques. The main animal model used is songbirds, one of the few vertebrate groups that evolved the ability to learn vocalizations. The overall goal of the research is to advance knowledge of the neural mechanisms for vocal learning and basic mechanisms of brain function.

Lab page: http://jarvislab.net/

1mb long DNA with Nanopore technology

Jit — Tue, 19 Dec 2017 18:49:28 -0600

The first continuous DNA read of more than a million bases (>1Mb) has been achieved, using Oxford Nanopore sequencing technology. Congratulations to Martin Smith and collaborators! Read more: http://bit.ly/2j5TNCO

Professor and Associate Professors (PB-IV) Assistant Professors (PB-III) Job at IIIT, Allahabad

Mon, 31 Mar 2014 08:09:07 -0500

Indian Institute of Information Technology, Allahabad
Devghat, Jhalwa, Allahabad – 211012, Uttar Pradesh, India
E-mail: contact@iiita.ac.in, faculty.applications@iiita.ac.in
Web: www.iiita.ac.in Phone : 0532-2922031/27/67

Applications are invited on prescribed format along with self attested copies of the certificates for Faculty Positions in the following areas:
Sciences – Systems Biology, Computer Aided Drug Designing, Statistics, Applied Mathematics, Applied Physics. BioMedical Engineering – BioMechanics, BioMedical Instrumentation.

Last Date : May 10, 2014

Details are available on our website : http://www.iiita.ac.in

http://www.iiita.ac.in/downloads/announcements/uploads/FACULTY_Advertisement_NO-FS-01_2014130.pdf

Pacasus: Correction of palindromes in long reads from PacBio and Nanopore

BioStar — Mon, 12 Nov 2018 05:26:48 -0600

Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source folder: https://github.com/swarris/Pacasus/blob/master/vib2017.pdf.

The prepint version is found on http://www.biorxiv.org/content/early/2017/08/09/173872

It uses the pyPaSWAS framework for sequence alignment (https://github.com/swarris/pyPaSWAS)

Address of the bookmark: https://github.com/swarris/Pacasus

Find certain files/documents in Linux OS

Rahul Nayak — Sun, 06 Apr 2014 23:56:18 -0500

As bioinformatician I know the fact that we usually handle the large dataset and lost in the huge numbers of files and folders. In order to search the missing file a strong search command is required. The Linux Find Command is one of the most important and much used command in Linux sytems. Find command used to search and locate list of files and directories based on conditions you specify for files that match the arguments. Find can be used in variety of conditions like you can find files by permissions, users, groups, file type, date, size and other possible criteria.

Through this article we are sharing our day-to-day Linux find command experience and its usage in the form of examples. In this article we will show you the most used 35 Find Commands examples in Linux. We have divided the section into Five parts from basic to advance usage of find command.

Part I – Basic Find Commands for Finding Files with Names
1. Find Files Using Name in Current Directory

Find all the files whose name is gene.txt in a current working directory.

# find . -name gene.txt

./gene.txt

2. Find Files Under Home Directory

Find all the files under /home directory with name gene.txt.

# find /home -name gene.txt

/home/gene.txt

3. Find Files Using Name and Ignoring Case

Find all the files whose name is gene.txt and contains both capital and small letters in /home directory.

# find /home -iname gene.txt

./gene.txt
./Gene.txt

4. Find Directories Using Name

Find all directories whose name is Gene in / directory.

# find / -type d -name Gene

/Gene

5. Find fasta Files Using Name

Find all php files whose name is gene.fasta in a current working directory.

# find . -type f -name gene.fasta

./gene.fasta

6. Find all PHP Files in Directory

Find all fasta files in a directory.

# find . -type f -name "*.fasta"

./gene.fasta
./cancer.fasta
./allgene.fasta

Part II – Find Files Based on their Permissions
7. Find Files With 777 Permissions

Find all the files whose permissions are 777.

# find . -type f -perm 0777 -print

8. Find Files Without 777 Permissions

Find all the files without permission 777.

# find / -type f ! -perm 777

9. Find SGID Files with 644 Permissions

Find all the SGID bit files whose permissions set to 644.

# find / -perm 2644

10. Find Sticky Bit Files with 551 Permissions

Find all the Sticky Bit set files whose permission are 551.

# find / -perm 1551

11. Find SUID Files

Find all SUID set files.

# find / -perm /u=s

12. Find SGID Files

Find all SGID set files.

# find / -perm /g+s

13. Find Read Only Files

Find all Read Only files.

# find / -perm /u=r

14. Find Executable Files

Find all Executable files.

# find / -perm /a=x

15. Find Files with 777 Permissions and Chmod to 644

Find all 777 permission files and use chmod command to set permissions to 644.

# find / -type f -perm 0777 -print -exec chmod 644 {} \;

16. Find Directories with 777 Permissions and Chmod to 755

Find all 777 permission directories and use chmod command to set permissions to 755.

# find / -type d -perm 777 -print -exec chmod 755 {} \;

17. Find and remove single File

To find a single file called gene.txt and remove it.

# find . -type f -name "gene.txt" -exec rm -f {} \;

18. Find and remove Multiple File

To find and remove multiple files such as .fa or .gb, then use.

# find . -type f -name "*.fa" -exec rm -f {} \;

OR

# find . -type f -name "*.gb" -exec rm -f {} \;

19. Find all Empty Files

To file all empty files under certain path.

# find /tmp -type f -empty

20. Find all Empty Directories

To file all empty directories under certain path.

# find /tmp -type d -empty

21. File all Hidden Files

To find all hidden files, use below command.

# find /tmp -type f -name ".*"

Part III – Search Files Based On Owners and Groups
22. Find Single File Based on User

To find all or single file called gene.txt under / root directory of owner root.

# find / -user root -name gene.txt

23. Find all Files Based on User

To find all files that belongs to user Rahul under /home directory.

# find /home -user rahul

24. Find all Files Based on Group

To find all files that belongs to group Developer under /home directory.

# find /home -group developer

25. Find Particular Files of User

To find all .txt files of user Rahul under /home directory.

# find /home -user rahul -iname "*.txt"

Part IV – Find Files and Directories Based on Date and Time
26. Find Last 50 Days Modified Files

To find all the files which are modified 50 days back.

# find / -mtime 50

27. Find Last 50 Days Accessed Files

To find all the files which are accessed 50 days back.

# find / -atime 50

28. Find Last 50-100 Days Modified Files

To find all the files which are modified more than 50 days back and less than 100 days.

# find / -mtime +50 –mtime -100

29. Find Changed Files in Last 1 Hour

To find all the files which are changed in last 1 hour.

# find / -cmin -60

30. Find Modified Files in Last 1 Hour

To find all the files which are modified in last 1 hour.

# find / -mmin -60

31. Find Accessed Files in Last 1 Hour

To find all the files which are accessed in last 1 hour.

# find / -amin -60

Part V – Find Files and Directories Based on Size
32. Find 50MB Files

To find all 50MB files, use.

# find / -size 50M

33. Find Size between 50MB – 100MB

To find all the files which are greater than 50MB and less than 100MB.

# find / -size +50M -size -100M

34. Find and Delete 100MB Files

To find all 100MB files and delete them using one single command.

# find / -size +100M -exec rm -rf {} \;

35. Find Specific Files and Delete

Find all .gb files with more than 10MB and delete them using one single command.

# find / -type f -name *.gb -size +10M -exec rm {} \;