BOL: All Site Activity

All Site Activity

- Nadia Baig@Nadia
Nadia Baig joined the group Comparative Genomics !! 2005 days ago
- Nadia Baig@Nadia
Nadia Baig answered the question WHich method is best to convert pacBio reads in .sra format to .fastq format? 2005 days ago

Okay I will try thanks.
- Archana Malhotra@archana
Archana Malhotra commented on an answer to a question 2005 days ago

Try HECIL, a new long read correction tool. https://github.com/NDBL/HECIL
- Rahul Nayak@rahul
Rahul Nayak is now a friend with Nadia Baig 2005 days ago
Rahul Nayak@rahul
Nadia Baig@Nadia
- Nadia Baig@Nadia
Nadia Baig is now a friend with Rahul Nayak 2005 days ago
Nadia Baig@Nadia
Rahul Nayak@rahul
- Jit@jit.aber
Jit bookmarked snakepipes: A toolkit based on snakemake and python for analysis of NGS data 2005 days ago

snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data. DNA-mapping* ChIP-seq* RNA-seq* ATAC-seq* scRNA-seq Hi-C Whole Genome Bisulfite Seq/WGBS (*Also available in...

https://github.com/maxplanck-ie/snakepipes
- Jit@jit.aber
Jit posted to the wire 2005 days ago

What is Comparative Genomics? https://www.news-medical.net/life-sciences/What-is-Comparative-Genomics.aspx #Comparative #Genomics
- BioStar@biostar
BioStar posted to the wire 2006 days ago

Bioinformatics internship https://internshala.com/internship/detail/bioinformatics-internship-in-bangalore-at-bayeslabs1559038161 #Bioinformatics #Internship #Bangalore #bayeslabs
- Nadia Baig@Nadia
Nadia Baig commented on an answer to a question 2006 days ago

fastq-dump --split-spot path/to/local/file/SRR649944.sra
- Neel@neelam
Neel commented on an answer to a question 2006 days ago

I always prefer EBI: This way is better than fastq-dump. EBI has fastq files to squarely download and use. got to EBI http://www.ebi.ac.uk/ena/data/view/SRR121576 replace SRR121576 with your id name. By the way , did you...
- Archana Malhotra@archana
Archana Malhotra answered the question How to install LoRDEC? 2006 days ago

Try HECIL, a new long read correction tool. https://github.com/NDBL/HECIL
- Neel@neelam
Neel commented on an answer to a question 2006 days ago

I always prefer EBI: This way is better than fastq-dump. EBI has fastq files to squarely download and use. got to EBI http://www.ebi.ac.uk/ena/data/view/SRR121576 replace SRR121576 with your id name. By the way , did you...
- Nadia Baig@Nadia
Nadia Baig answered the question How to install LoRDEC? 2006 days ago

Thanks neelam. To install HALC both BLASR and Lordec are needed.
- Neel@neelam
Neel answered the question WHich method is best to convert pacBio reads in .sra format to .fastq format? 2006 days ago

I always prefer EBI: This way is better than fastq-dump. EBI has fastq files to squarely download and use. got to EBI http://www.ebi.ac.uk/ena/data/view/SRR121576 replace SRR121576 with your id name. By the way , did you...
- Neel@neelam
Neel answered the question How to install LoRDEC? 2006 days ago

It is certainly off topic, but HALC is the best choice for correction of long PacBio reads, when both, read size and quality, are the main focus of the analysis. Lordec is not very useful and surprisingly...
- Nadia Baig@Nadia
Nadia Baig answered the question WHich method is best to convert pacBio reads in .sra format to .fastq format? 2008 days ago

fastq-dump --split-spot path/to/local/file/SRR649944.sra
- Rahul Nayak@rahul
Rahul Nayak answered the question WHich method is best to convert pacBio reads in .sra format to .fastq format? 2008 days ago

Can you please share your command used ?
- Rahul Nayak@rahul
Rahul Nayak commented on an answer to a question 2008 days ago

You might need to install libboost (I presume you are using Ubuntu) sudo apt-get install libboost-dev
- Nadia Baig@Nadia
Nadia Baig asked WHich method is best to convert pacBio reads in .sra format to .fastq format? 2008 days ago

i am using fastq dump to convert sra files into fastq. In case of fastq this tool gives me a message on terminal "Ignoring --- number of reads as the spot length is less than 1"). if my sra file is of 6GBs, i always get fastq file less than the...
- Jit@jit.aber
Jit commented on an answer to a question 2008 days ago

You can try this script https://github.com/jnarayan81/BioScripts/blob/master/runMapper.sh to map long reads.

BOL

Our Sponsors

All Site Activity