User: sbdk82

gravatar for sbdk82
sbdk8240
Reputation:
40
Status:
New User
Location:
United States
Last seen:
3 months, 2 weeks ago
Joined:
4 years, 9 months ago
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s*****@gmail.com

Posts by sbdk82

<prev • 46 results • page 1 of 5 • next >
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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 3 months ago by sbdk8240
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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 4 months ago by sbdk8240 • updated 3 months ago by Biostar ♦♦ 20
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sequence alignment using edlib c++ library
... I am using [edlib][1] library for sequence alignment using edit (Levenshtein) distance. It says that its infix(HW) alignment method does not penalize the start and end gaps. But it does not output the correct result when I use HW mode. #include #include "edlib.h" int main() { ...
alignment c++ written 7 months ago by sbdk8240
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Running DSK for multiple k values
... I am running DSK for counting k-mers for k=31, 47, 63 and 79. I could not figure out if there is a way to run DSK once for all k values. Is there an option for that? Can I get the frequency histogram without counting the k-mers? ...
k-mer written 9 months ago by sbdk8240
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Running k-mer counting tool DSK with multiple k values
... I am running DSK for counting k-mers for k=31, 47, 63 and 79. I could not figure out if there is a way to run DSK once for all k values. Is there an option for that? ...
k-mer sequence written 10 months ago by sbdk8240
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Comment: C: Consensus by aligning and extending the sequences
... Thanks !! I will try them ...
written 18 months ago by sbdk8240
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Consensus by aligning and extending the sequences
... I am trying to align and extend some sequences to get a larger consensus sequence. Here is a toy example of my problem ACTTACTGTAGTAGA GTA-AGATGCGATGAGGAGAT-GAGAAATG GATG--ATGAGGAGATAGAGAAATGATTATA ---------------------------------------------- AC ...
fasta alignment msa written 18 months ago by sbdk8240 • updated 18 months ago by h.mon24k
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Comment: C: Mismatch and Indel statistics from BAM/SAM file
... It worked fine except the BAM files generated by [LAST][1] [1]: http://last.cbrc.jp/ ...
written 19 months ago by sbdk8240
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Comment: C: Mismatch and Indel statistics from BAM/SAM file
... Yes, it is from nanopore. I am trying to align naopore reads against both illumina and Pacbio contigs ...
written 19 months ago by sbdk8240
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Mismatch and Indel rate in alignment
... I am using BWA to align the raw reads against a contig set. I would like to know the overall mismatch rate as well as indels in the entire alignment (SAM/BAM). I tried various options of samtools/bamtools, but could not able to find this. ...
alignment sam bam written 19 months ago by sbdk8240 • updated 19 months ago by prasundutta87330

Latest awards to sbdk82

Epic Question 11 months ago, created a question with more than 10,000 views. For Tophat Error : Couldn't build bowtie index with err = 1
Popular Question 11 months ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Popular Question 12 months ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Popular Question 14 months ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Great Question 2.6 years ago, created a question with more than 5,000 views. For Tophat with Bowtie2 long index
Popular Question 2.6 years ago, created a question with more than 1,000 views. For RNA-Seq analysis and expression level
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Great Question 3.6 years ago, created a question with more than 5,000 views. For Tophat Error : Couldn't build bowtie index with err = 1
Popular Question 3.6 years ago, created a question with more than 1,000 views. For extracting sequence from large fasta file
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Tophat with Bowtie2 long index
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Tophat Error : Couldn't build bowtie index with err = 1
Popular Question 4.2 years ago, created a question with more than 1,000 views. For cufflink and cuffmerge error

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