User: sbdk

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sbdk60
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6 months ago
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Posts by sbdk

<prev • 54 results • page 1 of 6 • next >
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Extract Info from chromosome locations
... I have some data that needs to be analyzed which contains species name, chromosome number, start and end locations like `hg19,chr2:144709344-144709495` I just need to get to know if it is present a coding region or part of intron or UTR or upstream/downstream of a gene. Is there a quick way to get ...
gene chromosome written 9 months ago by sbdk60
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Comment: C: CD-HIT Clustering evaluation
... Could you please point me to the script that I can use for comparing clustering results with the benchmark? I have my clustering as well as the benchmark in the following tsv format (clusterId \t Name) 0 AT4G16950_0 0 AT4G16950_2 0 AT4G16950_1 1 AT2G20950_1 ...
written 10 months ago by sbdk60
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Comment: C: Download all isoforms
... Thanks !! I tried to download from [TAIR][1] and Uniport database (as replied to an earlier comment). I hope I am on right track. [1]: https://www.arabidopsis.org/index.jsp ...
written 10 months ago by sbdk60
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Comment: C: Download all isoforms
... I downloaded the `pep.fasta` and `cdna.fasta` from [here][1]. For some other organisms, I am getting sequences from [Uniport][2]->Components->Downloads->FASTA format(canonical and isoform). Am I doing it right? [1]: https://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_fil ...
written 10 months ago by sbdk60
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Comment: C: CD-HIT Clustering evaluation
... Thanks. This is useful. I just wrote a program to do that task, but using `awk` is much easier. ...
written 10 months ago by sbdk60
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Comment: C: CD-HIT Clustering evaluation
... Thanks !! I will definitely try the MCL tool. ...
written 10 months ago by sbdk60
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CD-HIT Clustering evaluation
... I am using CD-HIT to cluster some protein sequences and I would like to evaluate the performance of the clustering for my dataset. Is there any tool for this provided I have a benchmarked clustering results for those sequences? Also, Is there any script available to collect the actual sequences fr ...
cd-hit clustering rna-seq sequencing written 10 months ago by sbdk60
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Download all isoforms
... I want to collect all isoforms of all genes (Fasta/Fastq file of nucleotide and protein sequences) of Arabidopsis. I am wondering if there is a straightforward way to download the file from any database. ...
sequence isoform written 10 months ago by sbdk60
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Comment: C: Blast - Formatting Output
... How can I get the `description` ( first column in the figure) when I run the command line blastp? ![blastp][1] [1]: http://i68.tinypic.com/9a34oo.jpg ...
written 2.1 years ago by sbdk60
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Running IsoSeq pipeline
... I am analyzing Pacbio data for the first time and I have the following files 1) ..fastq.gz 2) ...sts.xml 3) ...subreadset.xml 4) ...subreads.bam 5) ...subreads.bam.pb I am following the IsoSeq pipeline given [here][1]. I finished the "Generate CCS" step by executing "ccs" comm ...
isoseq pacbio written 2.2 years ago by sbdk60 • updated 12 weeks ago by Biostar ♦♦ 20

Latest awards to sbdk

Popular Question 7 months ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Great Question 2.1 years ago, created a question with more than 5,000 views. For Tophat with Bowtie2 long index
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Popular Question 2.1 years ago, created a question with more than 1,000 views. For extracting sequence from large fasta file
Epic Question 2.8 years ago, created a question with more than 10,000 views. For Tophat Error : Couldn't build bowtie index with err = 1
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Great Question 4.4 years ago, created a question with more than 5,000 views. For Tophat with Bowtie2 long index
Popular Question 4.4 years ago, created a question with more than 1,000 views. For RNA-Seq analysis and expression level
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Great Question 5.5 years ago, created a question with more than 5,000 views. For Tophat Error : Couldn't build bowtie index with err = 1
Popular Question 5.5 years ago, created a question with more than 1,000 views. For extracting sequence from large fasta file
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Tophat with Bowtie2 long index
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Tophat Error : Couldn't build bowtie index with err = 1
Popular Question 6.0 years ago, created a question with more than 1,000 views. For cufflink and cuffmerge error

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