User: Rohit

gravatar for Rohit
Rohit1.3k
Reputation:
1,260
Status:
Trusted
Location:
European union
Last seen:
1 week, 5 days ago
Joined:
4 years, 10 months ago
Email:
s**********@gmail.com

Computational biologist analyzing non-model organisms

Posts by Rohit

<prev • 234 results • page 1 of 24 • next >
1
vote
0
answers
234
views
0
answers
Comment: C: How can I right align InDels ?
... Is there a particular reason that last of the A in the homopolymer is pushed in the middle of the indel and the indels are not clustered together? I might be naive, wouldn't the moving of the indels remove all the sense from the alignment. I wouldn't change the alignments without looking into the r ...
written 3 months ago by Rohit1.3k
1
vote
2
answers
376
views
2
answers
Comment: C: Assembling PacBio reads using a reference genome
... I personally do not know any reference guided pacbio assemblers. You can 1) Map the reads to the reference, go for local assemblies and then scaffold based on the complete set of pacbio reads 2) de novo assemble everything, then scaffold using the reference The 2nd option is better since if ther ...
written 3 months ago by Rohit1.3k
1
vote
1
answer
202
views
1
answers
Answer: C: empty SAM file
... Isn't the command `bowtie -m 1 -S bowtie_index/mm10 Oct4.fastq Oct4.sam` You don't need a directed output ">" ...
written 3 months ago by Rohit1.3k
0
votes
1
answer
274
views
1
answers
Comment: C: Closest gene to set of intervals
... You would need a bed file of [gene boundaries][1] for this [1]: ftp://ftp.ensembl.org/pub/release-89/gff3/homo_sapiens ...
written 3 months ago by Rohit1.3k
0
votes
1
answer
231
views
1
answers
Comment: C: LASTZ does not accept/like "-" (dash) in Fasta file
... I agree, this would destroy the original file - horrible experiences with sed -i and grep > (instead of grep '>') ...
written 3 months ago by Rohit1.3k
1
vote
1
answer
231
views
1
answers
Comment: C: LASTZ does not accept/like "-" (dash) in Fasta file
... You can use sed to replace the file first, `sed -e '/^[agctn]/ s/-/n/g' file1.fa >file2.fa` Additionally you have to use the --ambiguous=n and query.fa[unmask] options since you have lower-case letters. ...
written 3 months ago by Rohit1.3k
0
votes
1
answer
274
views
1
answers
Answer: A: Closest gene to set of intervals
... I am not sure if you have tried, bedtools [closest][1] already does everything (apart from name extraction) what you need. You can use the -D or -d options with -ref (with respect to reference) to check which is the closest with/without direction involved. [1]: http://bedtools.readthedocs.io/en/ ...
written 3 months ago by Rohit1.3k
0
votes
2
answers
292
views
2
answers
Comment: C: Help with finding introns
... Intron needs to be defined according to the gene boundary the cdna falls in, so you would need the gene boundary along with the cdna coordinates ...
written 3 months ago by Rohit1.3k
0
votes
2
answers
292
views
2
answers
Comment: C: Help with finding introns
... You might not be able to get the intron sequences from a fasta file with only cDNA. You need a bed/gff [file][1] with gene boundaries for the cDNA you are interested in and then you extract the regions that [are not][2] cDNA. Just keep in mind that your gene boundaries need to start and end with the ...
written 3 months ago by Rohit1.3k
1
vote
0
answers
853
views
0
answers
Comment: C: Gene lists and calculated Ka/Ks ratio per gene
... Since Ka/Ks ratios are compared to for a reference species with respect to another, which species do you want to compare it to? Ensembl has the calculated dN/dS in their ortholog comparison for each of the genes searched, also ensembl biomart has the calculated dN and dS (seperately) for the ortholo ...
written 3 months ago by Rohit1.3k

Latest awards to Rohit

Great Question 22 days ago, created a question with more than 5,000 views. For Best Hits From Blast Tabular Output Of Multiple-Queries
Appreciated 22 days ago, created a post with more than 5 votes. For A: Fastqc Over-Represented Sequences Are Adapters ?
Scholar 10 weeks ago, created an answer that has been accepted. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: RNA seq assembly and CEGMA
Popular Question 4 months ago, created a question with more than 1,000 views. For Kmer Frequency Distribution And Genome Complexity
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
Guru 6 months ago, received more than 100 upvotes.
Scholar 10 months ago, created an answer that has been accepted. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
Popular Question 11 months ago, created a question with more than 1,000 views. For Kmer Frequency Distribution And Genome Complexity
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
Popular Question 15 months ago, created a question with more than 1,000 views. For Kmer Frequency Distribution And Genome Complexity
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Introducing Reputation Threshold For Creating New Tags.
Autobiographer 17 months ago, has more than 80 characters in the information field of the user's profile.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Introducing Reputation Threshold For Creating New Tags.
Centurion 17 months ago, created 100 posts.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Introducing Reputation Threshold For Creating New Tags.
Scholar 17 months ago, created an answer that has been accepted. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
Voter 17 months ago, voted more than 100 times.
Great Question 23 months ago, created a question with more than 5,000 views. For Best Hits From Blast Tabular Output Of Multiple-Queries
Student 23 months ago, asked a question with at least 3 up-votes. For Best Hits From Blast Tabular Output Of Multiple-Queries
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Problem With Sam To Bam Converison After Alignment Of Scaffolds To Reference
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Best Hits From Blast Tabular Output Of Multiple-Queries
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Compare A Denovo Assembly To The Reference Genome
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Is It A Good Idea To Trim Rna-Seq Reads Or Just Remove N'S?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1390 users visited in the last hour