User: sbdk82
sbdk82 • 60
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Posts by sbdk82
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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 12 months ago by
sbdk82 • 60
3
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0
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725
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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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... 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 16 months ago by
sbdk82 • 60
0
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... 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 18 months ago by
sbdk82 • 60
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0
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... 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 19 months ago by
sbdk82 • 60
0
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1
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567
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1
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... Thanks !! I will try them ...
written 2.2 years ago by
sbdk82 • 60
0
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1
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567
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1
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... 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 ...
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... It worked fine except the BAM files generated by [LAST][1]
[1]: http://last.cbrc.jp/ ...
written 2.3 years ago by
sbdk82 • 60
0
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3
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3.6k
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3
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... Yes, it is from nanopore. I am trying to align naopore reads against both illumina and Pacbio contigs ...
written 2.3 years ago by
sbdk82 • 60
1
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1
answer
1.3k
views
1
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... 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 2.3 years ago by
sbdk82 • 60
• updated
2.3 years ago by
prasundutta87 • 360
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