User: sbdk
sbdk • 60
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Posts by sbdk
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... 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 ...
written 9 months ago by
sbdk • 60
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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
sbdk • 60
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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
sbdk • 60
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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
sbdk • 60
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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
sbdk • 60
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Comment:
C: CD-HIT Clustering evaluation
... Thanks !! I will definitely try the MCL tool. ...
written 10 months ago by
sbdk • 60
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... 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 ...
written 10 months ago by
sbdk • 60
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... 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.
...
written 10 months ago by
sbdk • 60
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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
sbdk • 60
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... 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 ...
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5.5 years ago,
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For Tophat with Bowtie2 long index
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