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- Jit@jit.aber
Jit posted to the wire 3392 days ago

Understanding MegaBlast https://gordonlab.wustl.edu/btheta/blast/docs/megablast_readme.html #Blast #BLASTn #MegaBlast #Alignment
- Jit@jit.aber
Jit posted to the wire 3392 days ago

Whole-Genome Sequencing (WGS) PPT http://www.bx.psu.edu/~ratan/Sequence%20Analysis.pdf #PPT #WGS #Ratan
- Jit@jit.aber
Jit answered the question How to print only the first best hit from blastn tool? 3392 days ago

If you have > Blast 2.2.29 versions, then you need to put -max_hsps 1 parameter, and it gonna work well for you.
- Marysia@marysia
Marysia asked How to print only the first best hit from blastn tool? 3392 days ago

I used the following command to print the blast hit. [Terminal] blastn -query aaa.fa -db blastdb/nt -evalue 10e-5 -num_threads 4 -max_target_seqs 1 -outfmt '6 qseqid staxid qstart qend sallseqi sstart send evalue length frames qcovs' -out...
- Jit@jit.aber
Jit posted to the wire 3392 days ago

SAM flags https://broadinstitute.github.io/picard/explain-flags.html #SAM #Flags
- Bulbul@bulbul
Bulbul posted a new ad in the Opportunity Bioinformatics walk-in-interview at Tezpur University 3392 days ago
- Bulbul@bulbul
Bulbul posted a new ad in the Opportunity Bioinformatics opening at ICGEB NEW DELHI 3392 days ago
- Nihal Babu@nihalb
Nihal Babu posted a new ad in the Opportunity National workshop on Next Generation Sequencing 3392 days ago
- Jay Desai@jay4443
Jay Desai is now a friend with Jitendra Narayan 3392 days ago
Jay Desai@jay4443
Jitendra Narayan@admin
- Jitendra Narayan@admin
Jitendra Narayan is now a friend with Jay Desai 3392 days ago
Jitendra Narayan@admin
Jay Desai@jay4443
- Aishwarya Rasal@Aishwarya
Aishwarya Rasal is now a friend with Jitendra Narayan 3392 days ago
Aishwarya Rasal@Aishwarya
Jitendra Narayan@admin
- Jitendra Narayan@admin
Jitendra Narayan is now a friend with Aishwarya Rasal 3392 days ago
Jitendra Narayan@admin
Aishwarya Rasal@Aishwarya
- Shruti Paniwala@shruti
Shruti Paniwala posted to the wire 3392 days ago

Remove all blank lines from file. perl -i.bak -n -e "print if /\S/" ../finalSample.fa #Perl #Tricks #PerlOneliner
- Shruti Paniwala@shruti
Shruti Paniwala created a new bio-script Extracting FASTA sequences based on position with perl script !! 3392 days ago
- Jit@jit.aber
Jit posted to the wire 3393 days ago

SAM and BAM handling with Perl http://search.cpan.org/~lds/Bio-SamTools/lib/Bio/DB/Sam.pm # Perl #SAM #BAM
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh bookmarked DIAL 3393 days ago

A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to...

http://www.bx.psu.edu/miller_lab/
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh bookmarked Laj: viewing and manipulating the output from pairwise alignment programs 3393 days ago

Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and...

http://www.bx.psu.edu/~ratan/
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh bookmarked YASRA: Reference based assembler 3393 days ago

YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, which can differ substantially from the genome being sequenced. Mapping reads to reference genomes makes use of LASTZ (Harris et al), a...

https://github.com/aakrosh/YASRA
- Jit@jit.aber
Jit posted to the wire 3394 days ago

#Download #blastDB #locally. $ wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.*.tar.gz" for NT and wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz" for NR
- Jit@jit.aber
Jit posted to the wire 3394 days ago

Split the bam file by chromosome. $ bamtools split -in file.bam -reference #Split #Bam #Bamtools

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