User: Kenny
Kenny • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- New York
- Last seen:
- 1 year, 10 months ago
- Joined:
- 2 years, 1 month ago
- Email:
- k*****@nyu.edu
Posts by Kenny
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• 17 results •
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2
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... Hi all,
I did a reverse BLAST where my trancriptome is the database and my scaffold is the query. The reason why I do this is to see where the transcripts fall in the genome and if there are a lot of intron-like gaps.
When I look at the output, I found that some transcripts appear in more than one ...
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Comment:
C: gmap_build database problem
... Yes, now I want to output the mapping file (gff3) file and load it in IGV.
gmap -d oenopla_scaffold --format=2 -t 20 oenopla_transcriptome_subsetted_120617.fasta
...
written 23 months ago by
Kenny • 20
9
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4
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6 follow
4
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... Hi all,
I don't know if this should be posted here since this is not about data analysis or other bioinformatics work, but instead just a simple question about what to put in the resume.
I have used the following programs throughout my undergrad and graduate life. My question is:
1) Is it a good ...
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1
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553
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1
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... I have a scaffold genome and transcriptome of an organism. I have blast the transcriptome against the genome. When I checked the blast output, for example, one transcript appears in different scaffolds. Another example, one transcript appear in the same scaffold but there are gaps. I guess there mig ...
written 23 months ago by
Kenny • 20
2
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1
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553
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1
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... Hi all,
I would like to do gene annotation on my genome assembly. My PI wants me to use intron aware aligner and I found the following programs:
Apollo ([http://genomearchitect.github.io/][1])
Rail-RNA ([http://docs.rail.bio/][2])
Have someone used the above programs before? Do you have any oth ...
written 23 months ago by
Kenny • 20
• updated
23 months ago by
Puli Chandramouli Reddy • 180
0
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549
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Comment:
C: Adding sequence length to its ID
... It works perfectly. Thank you Pierre! ...
written 23 months ago by
Kenny • 20
2
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1
answer
549
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1
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... Hi all,
I have a scaffold sequence named "oenopla_scaffold_112117.fa" and it has 192947 sequences.
The ID of the scaffolds are:
grep ">" oenopla_scaffold_112117.fa | head -5
>scaffold_0
>scaffold_1
>scaffold_2
>scaffold_3
>scaffold_4
And the length of th ...
written 23 months ago by
Kenny • 20
• updated
23 months ago by
Pierre Lindenbaum ♦ 124k
0
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2
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2
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... You're right. My fastq file has odd number of reads :(
zcat TSSLR-BDA11_LongRead.fastq.gz | echo $((`wc -l`/4))
198625
...
written 2.1 years ago by
Kenny • 20
0
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... Dear all,
I have one illumina TruSeq long read assembly and three MiSeq 2x75 short reads assemblies. I want to merge the long read assembly to each of the short reads assemblies so that at the end I will have three total assmblies:
1) Long read scaffold + Velvet scaffolds
2) Long read scaffold + ...
written 2.1 years ago by
Kenny • 20
0
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1
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854
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1
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... I am currently running velvet on my velvet_hybrid.fasta file. My command is:
for k in {93..131..2}; do velveth ./Velvet_VelvetContigs/k$k $k -long -fasta Velvet_Hybrid.fasta; velvetg ./Velvet_VelvetContigs/k$k -ins_length auto -exp_cov auto -cov_cutoff auto -read_trkg yes; done
However, I get ...
written 2.1 years ago by
Kenny • 20
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