User: sbdk82
sbdk82 • 40
- Reputation:
- 40
- Status:
- New User
- Location:
- United States
- Last seen:
- 3 months, 2 weeks ago
- Joined:
- 4 years, 9 months ago
- Email:
- s*****@gmail.com
Posts by sbdk82
<prev
• 46 results •
page 1 of 5 •
next >
0
votes
2
answers
87k
views
2
answers
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
sbdk82 • 40
0
votes
0
answers
298
views
0
answers
... 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 ...
0
votes
0
answers
215
views
0
answers
... 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() {
...
written 7 months ago by
sbdk82 • 40
0
votes
0
answers
298
views
0
answers
... 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?
...
written 9 months ago by
sbdk82 • 40
0
votes
0
answers
227
views
0
answers
... 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? ...
written 10 months ago by
sbdk82 • 40
0
votes
1
answer
431
views
1
answers
... Thanks !! I will try them ...
written 18 months ago by
sbdk82 • 40
0
votes
1
answer
431
views
1
answer
... 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 ...
0
votes
3
answers
2.6k
views
3
answers
... It worked fine except the BAM files generated by [LAST][1]
[1]: http://last.cbrc.jp/ ...
written 19 months ago by
sbdk82 • 40
0
votes
3
answers
2.6k
views
3
answers
... Yes, it is from nanopore. I am trying to align naopore reads against both illumina and Pacbio contigs ...
written 19 months ago by
sbdk82 • 40
1
vote
1
answer
947
views
1
answer
... 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. ...
written 19 months ago by
sbdk82 • 40
• updated
19 months ago by
prasundutta87 • 330
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
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1347 users visited in the last hour