User: Bade

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Bade40
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40
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New User
Location:
United States
Last seen:
12 months ago
Joined:
7 years, 1 month ago
Email:
a**********@gmail.com

about me

Posts by Bade

<prev • 16 results • page 1 of 2 • next >
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Answer: A: miRNA target prediction tools
... Hi Shahzad, Although late, but I would like to add *sPARTA* that we use in our lab. It is very good for whole genome target discovery. sPARTA: https://github.com/atulkakrana/sPARTA Bade ...
written 22 months ago by Bade40
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Download fastq files from SRA database using biosample identifier
... Hi All, I have a list of biosample identifiers like SAMN01096167, SAMN01096168 and SAMN01096169. Is there anyway I can download FASTQ files from SRA database using these identifiers? Usually, I use fastq-dump with SRR identifiers to download files like this: > fastq-dump -A SRR1642913 --split-f ...
sra fastq written 3.1 years ago by Bade40 • updated 3.1 years ago by Jenez520
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Comment: C: How to get RNAfold (structure) output in text format
... The ASCII-art is what I meant. - Bade ...
written 3.3 years ago by Bade40
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How to get RNAfold (structure) output in text format
... Hi List, Is there any way to get RNAfold predicted secondary structure in text format? It provides a PDF and PNG file but is it possible to get something like structures in this figure: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3787264/figure/F3/][1] Bade [1]: http://www.ncbi.nlm.nih.gov/pm ...
mfold secondary structure rnafold written 3.3 years ago by Bade40 • updated 3.3 years ago by shenwei3564.9k
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Compute test-score statistical significance using control-scores from shuffled population
... I am not a statistician therefore need your help in computing statistical significance of my data. Suppose I have 2 baskets (B1 and B2) on a table each with mix of apple and oranges, and there are 10 such tables (T1 to T10. Now, I have computed the log-odd score of finding apples in B1 at all 10 tab ...
R hypothesis-testing statistical-significance written 3.6 years ago by Bade40
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Get percentile cutoff from bigwig files
... Hi Members, I have bigwig files with genome-wide signal values. And I need to compute the Xth percentile of these signal values. Is there any tool that can compute signal percentiles directly from bigwig files? For Ex - I want to know the 95th percentile of all signal values in a bigwig file. If n ...
bed wiggle bigwig rna-seq statistics written 3.7 years ago by Bade40 • updated 3.7 years ago by Alex Reynolds29k
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Answer: A: miRNA target prediction
... You might want to generate some PARE (Parallel analysis of read ends) data and use tools like sPARTA: https://github.com/atulkakrana/sPARTA.github Here is the link to full paper:http://nar.oxfordjournals.org/content/42/18/e139 If you can't generate PARE data, then predict targets, check sPARTA rea ...
written 4.1 years ago by Bade40
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Answer: A: How to map miRNA to transcripts of targeting genes ?
... You can try sPARTA, if working on plants. It's very fast and sensitive to secondary structures that miRNA and target form - https://github.com/atulkakrana/sPARTA.github Link to paper- http://nar.oxfordjournals.org/content/42/18/e139 Bade ...
written 4.1 years ago by Bade40
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Answer: A: Mirna Target Prediction
... You didn't mentioned for plants or animals. You can try:  sPARTA for plants - http://nar.oxfordjournals.org/content/42/18/e139 Download Link for sPARTA: https://github.com/atulkakrana/sPARTA.github miRZA for animals - http://www.nature.com/nmeth/journal/v10/n3/full/nmeth.2341.html miRZA download ...
written 4.1 years ago by Bade40
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de novo hybrid assembly of transcriptome - Illumina PE and PacBio Full-length reads
... Hi All, I did a transcriptome assembly of Illumina SE and PE reads using Trinity, but the N50 values for my assembly are very low. Here is the summary: Total trinity 'genes': 748144 Total trinity transcripts: 916206 Percent GC: 43.83 Contig N10: 1765 Contig N20: 1064 Contig N30: 677 Contig ...
latest illumina pacbio rna-seq assembly written 4.1 years ago by Bade40

Latest awards to Bade

Popular Question 22 months ago, created a question with more than 1,000 views. For Download fastq files from SRA database using biosample identifier
Popular Question 3.1 years ago, created a question with more than 1,000 views. For de novo hybrid assembly of transcriptome - Illumina PE and PacBio Full-length reads
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Error while converting SYMBOLS to ENTREZID - Bioconductor
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Error while converting SYMBOLS to ENTREZID - Bioconductor
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Select Probset With Median Expression From Redundant Probesets - Affy
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Affymetrix Data Using Mas5 Giving Large Fc Values

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