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User: sbdk82

gravatar for sbdk82
sbdk82 • 30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
1 day, 11 hours ago
Joined:
3 years, 12 months ago
Email:
s*****@gmail.com

Posts by sbdk82

<prev • 43 results • page 1 of 5 • next >
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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 1 day ago by sbdk82 • 30
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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 5 weeks ago by sbdk82 • 30
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Comment: C: Consensus by aligning and extending the sequences
... Thanks !! I will try them ...
written 9 months ago by sbdk82 • 30
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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 9 months ago by sbdk82 • 30 • updated 9 months ago by h.mon ♦ 15k
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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 9 months ago by sbdk82 • 30
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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 9 months ago by sbdk82 • 30
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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 9 months ago by sbdk82 • 30 • updated 9 months ago by prasundutta87 • 170
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Comment: C: Mismatch and Indel statistics from BAM/SAM file
... Is there an executable? I am getting error while compiling. ...
written 9 months ago by sbdk82 • 30
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Comment: C: Mismatch and Indel statistics from BAM/SAM file
... I am still getting a blank file. Please check the last two lines of sam file ...
written 9 months ago by sbdk82 • 30
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Comment: C: Mismatch and Indel statistics from BAM/SAM file
... 0d6893dc-57eb-4eaa-a1ad-406b4528cc6f 0 c12692/f5p5/989 132 60 10S12M1D30M2I9M1I6M2D39M1I10M2I6M1D17M1D12M1D1M2D11M1D10M1I12M1I67M4I21M2D24M2I11M3D18M1I24M1D26M1D11M5D26M1I8M1D2M1D22M1D4M2D25M1D8M1D2M2D33M1D15M4I12M1D22M2I23M2D6M1D4M2D10M1I25M3I5M3I2M1I7M1I22M4I10M3I11M6I4M1I11M1I5M2I4M2I3M1I4M3I ...
written 9 months ago by sbdk82 • 30 • updated 9 months ago by genomax ♦ 49k

Latest awards to sbdk82

Epic Question 11 weeks ago, created a question with more than 10,000 views. For Tophat Error : Couldn't build bowtie index with err = 1
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Popular Question 3 months ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Popular Question 5 months ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Popular Question 15 months ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Great Question 22 months ago, created a question with more than 5,000 views. For Tophat with Bowtie2 long index
Popular Question 22 months ago, created a question with more than 1,000 views. For RNA-Seq analysis and expression level
Popular Question 22 months ago, created a question with more than 1,000 views. For Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
Great Question 2.9 years ago, created a question with more than 5,000 views. For Tophat Error : Couldn't build bowtie index with err = 1
Popular Question 2.9 years ago, created a question with more than 1,000 views. For extracting sequence from large fasta file
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Tophat with Bowtie2 long index
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