User: sam

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sam130
Reputation:
130
Status:
New User
Location:
United States
Last seen:
5 years, 2 months ago
Joined:
5 years, 4 months ago
Email:
h*******@msu.edu

Posts by sam

<prev • 9 results • page 1 of 1 • next >
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Test for between trees
... Hello. Does anyone know of a program or a graph that could compare trees with one another to test whether one tree belongs to the other tree?     ...
sequence algorithms graph written 5.2 years ago by sam130 • updated 5.2 years ago by Brice Sarver3.2k
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Comment: C: kmers in rna-seq
... yes because I don't think we could use DESEQ for this problem given the fact that we are not trying to detect deferentially expressed genes here... ...
written 5.3 years ago by sam130
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kmers in rna-seq
... I have a set of kmer counts coming from 2 groups. The first and second group have 25 RNA-seq samples each. I'm interested in identifying kmers that appear to have counts that are different between the 2 groups. In other words, for example, i have the 3mer AAT counts for each sample in both groups. I ...
kmer rna-seq written 5.3 years ago by sam130 • updated 5.2 years ago by Biostar ♦♦ 20
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k-mer analysis in RNA-seq
... hello I have an RNA-seq time series experiment (4 time points) where at t=0 the sample gets infected with a virus. I'm interested in checking whether their is any correlation between the kmers and the viral load increase across the 4-time points. I compute the 2-mers up to 7-mers for each fastq fil ...
sequence rna-seq written 5.3 years ago by sam130 • updated 5.3 years ago by Nicolas Rosewick8.4k
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k-mer tools - probability based models
... I have recently been looking at different k-mer tools (E.g., jellyfish). They all perform well with different computational complexities. However, most of them are counting tools. I'm interested in a tool that finds k-mers that are more than expected (more of a probability-based approach). I was won ...
rna-seq k-mers written 5.3 years ago by sam130 • updated 5.3 years ago by edrezen720
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Comment: C: find similar sequences between different sources
... The sequences are not identical. Do you recommend setting a similarity threshold for 2 sequences to be identical? ...
written 5.3 years ago by sam130
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find similar sequences between different sources
... Hello, I have different sets of sequences from different sources (e.g. I have around 20 fasta files (each fasta file correspond to one source) where each fasta file contains around 1000 sequences). I'm interested in identifying sequences that are similar and appear in more than one fasta file. In ...
sequence rna-seq sequencing written 5.3 years ago by sam130 • updated 5.3 years ago by Prakki Rama2.3k
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Answer: A: RNAstar alignment segmentation fault
... I found what was the problem. When generating a genome index, this parameter must be changed to accommodate smaller genomes:   genomeSAindexNbases 14 int: length (bases) of the SA pre-indexing string. Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches ...
written 5.3 years ago by sam130
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RNAstar alignment segmentation fault
... Hello, I have a question regarding the RNA-star alignment program. I'm trying to map thousands of reads (~7000 sequences) against a fasta file containing a handful of sequences (~20 sequences). In order to do that in RNA-star, I had to generate a genome index based on the small fasta file that cont ...
rna-star alignment rna-seq written 5.3 years ago by sam130

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Scholar 5.3 years ago, created an answer that has been accepted. For A: RNAstar alignment segmentation fault

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