User: nilus1432

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nilus143230
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

<prev • 9 results • page 1 of 1 • next >
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Comment: C: 16S Sanger single end read assembly
... 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 nilus143230
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16S Sanger single end read assembly
... 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 ...
assembly 16s sequencing microbiome written 12 months ago by nilus143230
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Single end RNAseq data strandedness infer-experiment-py
... 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 > ...
rna-seq written 22 months ago by nilus143230 • updated 22 months ago by h.mon31k
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TCGA MAF files after migration to GDC
... 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 ...
maf tcga written 4.2 years ago by nilus143230 • updated 4.2 years ago by Andrew J. Rech0
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Variant calling for MNP
... 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 ...
rna-seq snp written 5.2 years ago by nilus143230 • updated 5.2 years ago by Len Trigg1.5k
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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 nilus143230
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Answer: A: Obtaining alignment from psiblast
... I already have local blast, I want formatted output, any idea?? ...
written 5.8 years ago by nilus143230
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Obtaining alignment from psiblast
... 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 ...
alignment sequence blast snp written 5.8 years ago by nilus143230 • updated 5.8 years ago by Siva1.7k
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Retrieve SIFT results using python and web server
... 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 ...
alignment sequence snp written 5.9 years ago by nilus143230

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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