User: thustar

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thustar100
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3 years, 8 months ago
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Posts by thustar

<prev • 32 results • page 1 of 4 • next >
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Comment: C: How to split paired end SRA file into 2 correct fastq files
... Thanks for your quick reply. One more question. In your recommended website, there are many options like `Fastq files (ftp)` and `Submitted files (ftp)`. Is there any difference? Which file should I download? ...
written 3.7 years ago by thustar100
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How to split paired end SRA file into 2 correct fastq files
... Hello Biostars! In my project, I have to convert several [SRA files][1] to fastq files. These SRA files are paired end. I read a previous [post][2] about how to use fastq-dump to do so. However, I am still confused about the split step. For example, after I ran `fastq-dump ERR011087.sra`, I got E ...
sra fastq next-gen written 3.7 years ago by thustar100 • updated 7 days ago by Carlo.Ga0
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Comment: C: How to use a fastq file from paired library layout
... oh, really? I do not agree with you. Could you please show me the link to the description? I did not notice that. ...
written 4.0 years ago by thustar100
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Comment: C: How to use a fastq file from paired library layout
... Yes, I use fastq-dump to convert sra file to fastq file. Do you mean that if I use fastq-dump directly, I will have a mistake? ...
written 4.0 years ago by thustar100
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How to use a fastq file from paired library layout
... Hi biostars! I want to assemble some reads from real dataset like http://sra.dnanexus.com/studies/ERP000108/runs. However, I am confused with the description of Accession ERR011087. It says, library layout: paired. I do not know what this "paired" means. The first 24 lines of ERR011087.fastq is @ ...
next-gen written 4.0 years ago by thustar100 • updated 4.0 years ago by qingxiangg40
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(Closed) Why is gc content in different genome different?
... Hi, biostars! Why is gc content in different genome different? For example, gc content in genome A is 52%, meanwhile gc content in genome B is 49%. Why gc content is related to species? Is there any biological explanation? Thanks ...
gc content genetics written 4.0 years ago by thustar100
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Comment: C: What is the range of coverage depth of bacteria from environment sample?
... Thanks a lot. I have written python script based on pysam by myself. The simulated short-gun reads could be assembled well. However, these short reads are error-free. It is still different from reality. I was wondering how to mimic the real error noise in the short reads, for example, how to mimic ...
written 4.0 years ago by thustar100
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Comment: C: What is the range of coverage depth of bacteria from environment sample?
... Thanks for provide much information. I am very interested in your previous work about simulation. I think I am doing similar task. Do you have a detailed report? It will be helpful to compare our results. Besides, The link you provide is about environmental bacteria community. It seems to concent ...
written 4.0 years ago by thustar100
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Comment: C: What is the range of coverage depth of bacteria from environment sample?
... Thanks. Where could I find such dataset? And could I find related statisitical report on the dataset? I want to simulate mostly because I want to have a groundtruth,i.e. I can know which genome an assembled sequence comes from. But in real data, if two or more genomes share some repeated subsequen ...
written 4.0 years ago by thustar100
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What is the range of coverage depth of bacteria from environment sample?
... Hi biostars! I want to do some simulation of short-gun sequencing of bacteria genome. However, I do not know the range of coverage depth of bacteria from a real sample. For example, the minimal, maximum, and average coverage depth in real data will be helpful. By the way, coverage depth is the conc ...
gene reads next-gen-seq assembly written 4.0 years ago by thustar100

Latest awards to thustar

Supporter 4.0 years ago, voted at least 25 times.
Scholar 4.1 years ago, created an answer that has been accepted. For A: Is there any method to download a complete genome fasta file of a certain specie

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