User: nilus1432
nilus1432 • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- Singapore
- Last seen:
- 1 year ago
- Joined:
- 5 years, 10 months ago
- Email:
- n********@yahoo.com
Posts by nilus1432
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... After quality trimming the read size is much smaller in certain cases. I think a way is to do search individual read wise before and after trimming and compare results. ...
written 12 months ago by
nilus1432 • 30
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... Hi,
I have a single-end 16S Sanger sequencing generated using two primers (27F and 785F). I want to identify bacterial strain using this data. How to analyse this data?
My initial attempts,
I tried to merge read from two primers but there are no overlapping sequences.
So,
1. Should I take a unio ...
written 12 months ago by
nilus1432 • 30
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... Hi all,
I have a single end RNAseq data and would like to understand the strandedness of the data.
1. From wet-lab input I know "Stranded cDNA library was generated by reverse transcribing the RNA molecules".
2. I used `infer-experiment-py`
The output is:
> This is SingleEnd Data
> ...
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... Where to find the latest recommended MAFs for TCGA? particularly after TCGA data has been moved to GDC.
1. There are no MAF files on the [GDC][1],
2. The [NCI wiki][2] lists set of [current and obsolete][3] maf files, but the links mentioned are not working now. (Also in archive many files which a ...
written 4.2 years ago by
nilus1432 • 30
• updated
4.2 years ago by
Andrew J. Rech • 0
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... Hi All,
I would like to know is there any program for variant calling for multiple-nucleotide polymorphisms. For eg. detecting cases like, Reference = 'ATA', Sample = 'GTC'.
thanks a lot
...
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Comment:
C: Obtaining alignment from psiblast
... Yes, this is what i am looking for. I tried buildali.pl on the psiblast output (version 2.2.30) which was run using "psiblast -query fasta -db database -num_iterations=3 -out out.align".
However, the buildali.pl terminates with a error
"Error in alignhits.pl: blast output file out.align truncated ...
written 5.8 years ago by
nilus1432 • 30
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... I already have local blast, I want formatted output, any idea??
...
written 5.8 years ago by
nilus1432 • 30
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2.7k
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... Hi everyone,
I am using stand alone version of Psi-blast.
I want to get just the query sequence followed by matched-hit sequences (both aligned) in fasta format.
How to do it in Biopython or stand alone blast.
1. Some posts suggest Mview: for some reason this solution i am not using
2. I can g ...
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... Hello Everyone,
I want to get results of SIFT from a set of aligned sequence using SIFT web server and python
SIFT site i am using is
http://sift.jcvi.org/www/SIFT_aligned_seqs_submit.html
I want to submit several alignments to this server and get scaled probabilities for each alignment using ...
written 5.9 years ago by
nilus1432 • 30
Latest awards to nilus1432
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Variant calling for MNP
Popular Question
3.5 years ago,
created a question with more than 1,000 views.
For Variant calling for MNP
Popular Question
3.5 years ago,
created a question with more than 1,000 views.
For Retrieve SIFT results using python and web server
Student
3.8 years ago,
asked a question with at least 3 up-votes.
For TCGA MAF files after migration to GDC
Popular Question
5.0 years ago,
created a question with more than 1,000 views.
For Obtaining alignment from psiblast
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