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Answer: Filter Genome for Specific Sites
Answer: Filter Genome for Specific Sites
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
The Biostar Herald for Monday, May 20, 2024
Answer: Generating Group/Cluster Lists from fastq files
The Biostar Herald for Monday, May 20, 2024
ClusterProfiler : What is GeneRatio and BgRatio?
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Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
GenoMax
142k
For those samples it appears that raw data was not submitted. Just an assembly. $ esearch -db biosample -query SAMN08009548 | elink -…
Comment: How can I calculate the OS of each patient?
by
Pedro
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**I have already tried this code. listSamples with HNSC cancer and smokers. I need at least one supporting material to find out the survi…
Comment: Filter Genome for Specific Sites
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Anita
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Great, thank you!
Comment: Filter Genome for Specific Sites
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Anita
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This is unhelpful and doesn't answer my question.
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
Harshita
• 0
It seems that the authors in this paper have used paired-end sequences only for their analysis, and for that, they would also have used the…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
Harshita
• 0
Thank you so much for helping me out in this! I have used most of the sequences that are found in this table. But, some samples like the…
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
GenoMax
142k
Looks like the samples are from this project: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320483&o=acc_s%3Aa This table has the SR…
Comment: Filter Genome for Specific Sites
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Pierre Lindenbaum
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> My sites are in an Excel file right now ![enter image description here][1] <!-- was an American educator and academic administrator…
Answer: Filter Genome for Specific Sites
by
GenoMax
142k
> I have a list of ~1,300 single bp sites Convert your file to plain text [**BED format**][1] (three fields required). Use `bedtools slo…
Comment: How to generate an Upset plot in R to plot the shared variants between cell free
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sainavyav22
• 0
It worked, Thank you very much!
Comment: What marks a De-Novo Genome assembly as FAILED?
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dthorbur
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I'm unsure you'll be able to identify whole chromosomes that are not core from illumina reads alone. That might be easier to do with a micr…
Comment: Error in using BioSampleParser tool: subscript out of bounds
by
Mohamed Samir
▴ 20
Dear marco, We need to ask ourselves why it is not working for all bioprojects ? I have looked into this, and observed that as long as the…
Comment: Why most genes have high padj values
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Ram
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You ***want*** ~3000 DE genes?<a href="" title="Text added because biostars parser needs it"></a>
Answer: Generating Group/Cluster Lists from fastq files
by
GenoMax
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> I was hoping to just do this in galaxy This is not a galaxy option but `clumpify.sh ` from BBMap suite can cluster sequences/dedupe th…
Comment: Practical Haplotype Graph v2 not finding correct paths
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beantkapoor16
▴ 10
Hello, just wanted to check in if the code has been fixed yet? Thank you.
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