User: Kenny

gravatar for Kenny
Kenny30
Reputation:
30
Status:
New User
Location:
New York
Last seen:
3 years ago
Joined:
3 years, 3 months ago
Email:
k*****@nyu.edu

Posts by Kenny

<prev • 17 results • page 1 of 2 • next >
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Same transcript appear on different scaffolds. Why?
... 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 ...
alignment written 3.1 years ago by Kenny30 • updated 3.1 years ago by Macspider3.3k
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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 3.1 years ago by Kenny30
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10 follow
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Forum: What computer skills should I put on my resume?
... 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 ...
genome forum resume written 3.1 years ago by Kenny30 • updated 4 months ago by keeley.mazurkiewicz50
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Comment: A: Some examples of Intron aware aligner?
... 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 3.1 years ago by Kenny30
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Some examples of Intron aware aligner?
... 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 ...
alignment written 3.1 years ago by Kenny30 • updated 3.1 years ago by Puli Chandramouli Reddy190
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Comment: C: Adding sequence length to its ID
... It works perfectly. Thank you Pierre! ...
written 3.1 years ago by Kenny30
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Adding sequence length to its ID
... 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 ...
sequence written 3.1 years ago by Kenny30 • updated 3.1 years ago by Pierre Lindenbaum133k
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Comment: C: DiscovarDenovo - fastq files should be interlaced
... You're right. My fastq file has odd number of reads :( zcat TSSLR-BDA11_LongRead.fastq.gz | echo $((`wc -l`/4)) 198625 ...
written 3.3 years ago by Kenny30
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Metassembler - config file
... Dear all, I have one illumina TruSeq long read assembly and three MiSeq 2x75 short reads assemblies. I want to merge the long read assembly to each of the short reads assemblies so that at the end I will have three total assmblies: 1) Long read scaffold + Velvet scaffolds 2) Long read scaffold + ...
assembly written 3.3 years ago by Kenny30
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Comment: C: Short-long read hybrid de novo assembly - determine k-mer size
... I am currently running velvet on my velvet_hybrid.fasta file. My command is: for k in {93..131..2}; do velveth ./Velvet_VelvetContigs/k$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 3.3 years ago by Kenny30

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