User: syrup16g_TO

gravatar for syrup16g_TO
syrup16g_TO40
Reputation:
40
Status:
New User
Location:
Japan
Last seen:
4 years, 9 months ago
Joined:
5 years, 11 months ago
Email:
t**********@gmail.com

Master of Engeneering ( Applied Physics )

Undergraduate student of Medicine.

Exome resequencing, RNA-seq, ChIP-seq, CLIP-seq. Protein structure prediction, in-silico drug screening.

Posts by syrup16g_TO

<prev • 17 results • page 1 of 2 • next >
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Comment: C: How to analyze non-Human whole genome re-sequencing data?
... Very thanks, airan. I used SnpEff, and felt it suitable for me. ...
written 4.8 years ago by syrup16g_TO40
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How to analyze non-Human whole genome re-sequencing data?
... Hi everyone,   We did whole-genome sequencing of a disease-model rat. We mapped reads on Rat genome(rn5), and called variants(SNVs, indels, SVs).   But we don't know the following way to analyze variants data. If sample were of human, we would annotate variants using DBs( 1000g, dbSNP, and so ...
snp sequencing written 4.8 years ago by syrup16g_TO40 • updated 4.8 years ago by iraun3.6k
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Annotation of Rat WGS data by AnnoVar
... I want to annotate Rat WGS data using AnnoVar software. WGS reads are mapped to rn5 reference. Therefore, I tried to use rn5 annotation of AnnoVar databases, but failed.   How can I use rn5 annotation? Please let me know, thanks. ...
genome annotation snp written 4.8 years ago by syrup16g_TO40 • updated 15 months ago by Biostar ♦♦ 20
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How to get ortholog sequences.
... Hi, everyone.   I want to get the sequence pair of ortholog. e.g. For AGO2, I want to get the human AGO2 amino-acid sequence and the rat AGO2 amino-acid sequence.   Thank you. ...
ortholog sequence written 4.9 years ago by syrup16g_TO40 • updated 4.9 years ago by cdsouthan1.8k
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Unmapped reads in BLAT output ( psl file )
... Hello, Please tell me about unmapped reads in BLAT run. If reads are not mapped to reference sequence by BLAT, what is written in output psl file? How do I extract unmapped reads? Thank you very much. ...
alignment blat written 5.2 years ago by syrup16g_TO40 • updated 5.2 years ago by Prakki Rama2.3k
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Comment: C: distances betweeen my SNV and nearest exon
... Excellent! Thank you very much! I got the way to measure the distance. ...
written 5.3 years ago by syrup16g_TO40
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distances betweeen my SNV and nearest exon
... Hello everyone.   I want to calculate the distances between detected intronic SNVs and nearest exons ( upstream/downstream ). However, I can do it only with very computationally-costful way.   Does anyone know more simple way? Any helps will be appretiated. Thank you. ...
exome annotation snp written 5.3 years ago by syrup16g_TO40 • updated 5.3 years ago by Devon Ryan91k
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Comment: C: Genomic Positions Of 3'Utrs Of Refseq-Genes
... Thank you for your reply! I've succeeded to get that information. ...
written 5.4 years ago by syrup16g_TO40
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Genomic Positions Of 3'Utrs Of Refseq-Genes
... Dear all, I want to get the genomic positions of 3'UTR of RefSeq genes, but I don't know how to get the information about 3'UTR. e.g. RefSeq_geneID chrXXX:start-end ( 3'UTR position ) Any helps would be much appreciated. Thank you. ...
refseq utr position written 5.4 years ago by syrup16g_TO40 • updated 5.4 years ago by dariober10k
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How To Calculate P-Value Of Circular Binary Segmentation?
... Hello everyone, I'm new to bioinformatics. I wrote a script that computes circular binary segmentation ( CBS ) in order to call a significant peak from ChIP-seq data. But I don't understand how to calculate the p-value of such peaks using CBS Tij value. Is anyone know the way? Thank you for your ...
p-value peak-calling written 5.5 years ago by syrup16g_TO40

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