User: Picasa

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Picasa270
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Posts by Picasa

<prev • 187 results • page 1 of 19 • next >
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Help for limma DE interpretation.
... Hi everybody. Maybe my questions will sound stupid but sorry I am a beginner in this domain: I am not sure about the interpretation of DE analysis from limma. My goal is to list the genes that are up and down regulated between 2 conditions (cond 1 and cond 2). cont.matrix <- makeContrast ...
rnaseq limma written 6 hours ago by Picasa270 • updated 3 hours ago by Devon Ryan60k
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Comment: C: PCA from kallisto output
... From what I understand, TPM is already normalized no ? The package you mentioned seems to recommend to apply `rlog` on counts data. ...
written 6 days ago by Picasa270
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PCA from kallisto output
... Hi, My goal is to plot a simple PCA to compare samples after kallisto run. I am a bit confuse how to do it. Should I take the "est_counts" or the "TPM" values ? ...
kallsito written 6 days ago by Picasa270 • updated 6 days ago by Lando Ringel430
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Comment: C: PCA tpm fpkm
... prcomp needs a matrix with genes as columns right ? ...
written 6 days ago by Picasa270
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Comment: A: blastn staxids returning N/A
... I got the same problem .. ...
written 10 days ago by Picasa270
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Comment: C: Any advice for a de novo genome assembly
... Hi Brian, Can you explain why normalization is more complicated when reads are in multiple libraries (so different insert size) ? ...
written 11 days ago by Picasa270
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Comment: C: What Is A Typical Salary Range For Bioinformatician In Singapore
... I hesitate to look for a job in Singapore; as I heard that life out there is expensive. Do you have more information about the salary nowadays ? ...
written 17 days ago by Picasa270
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Download Uniref ID though wget
... Hi, I would like to download the UNIREF 100 id http://www.uniprot.org/uniref/ and get at the end a file with: Cluser ID Common taxon ID We can download it though the button "Download" but since the file will be big (I think). I am wondering if there is a way to download it though "wget". ...
uniref written 20 days ago by Picasa270 • updated 15 days ago by Elisabeth Gasteiger1.0k
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BWA error [bns_restore_core] Parse error reading
... Hi, I have downloaded some bacteria genomes on ncbi and then I `cat` them. I have built an index with these genome after trying to map my reads I got this error: > [bns_restore_core] Parse error reading > db/contaminants.amb Someone know what is going on ? Thanks ...
bwa index written 29 days ago by Picasa270 • updated 29 days ago by Vijay Lakhujani560
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Read filtering strategy and BWA
... Hi, I have a list of sequences that are contaminant. I would like to map my reads to these contaminants and then extract the unmapped reads . For that I want to use BWA. But I have a doubt with an option. Should I use the -M option (mark shorter alignment as secondary) ? because I use the flag -f ...
contamination bwa written 4 weeks ago by Picasa270 • updated 4 weeks ago by Brian Bushnell9.0k

Latest awards to Picasa

Centurion 3 months ago, created 100 posts.
Student 4 months ago, asked a question with at least 3 up-votes. For Best strategy for de novo assembly with illumina reads ?
Supporter 6 months ago, voted at least 25 times.
Scholar 6 months ago, created an answer that has been accepted. For A: 16S Paired-End Illumina MiSeq Data in Qiime
Rising Star 7 months ago, created 50 posts within first three months of joining.

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