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education books

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project-management file-management

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Analyst Scientist

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r statistics python biopython

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genomics cram gatk galaxy

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biostars

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meta biostars

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Popular Question to emmanouil.a ▴ 120

Recent Replies

Answer: Bulk and Single Cell RNA-seq online course by swbarnes2 13k

I'd start by getting tutorials for R libraries like DESeq, EdgeR, Seurat, etc, and learn by doing.

Answer: gene set enrichment analysis- by enrichGO by Istvan Albert 99k

Some analyses compare a subset of genes to a background. In those cases you would need to select a subset via some attributes like pvalues …

Comment: Ipyrad de novo for variant calling by Betsy • 0

Were you ever able to resolve this error? I am having the exact same problem trying to run ipyrad on already demultiplexed fq.gz files

Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison by ATpoint 78k

Depends on the analysis. If you do some sort of gene ratio calculation then probably yes. Batch correction does not affect all genes equall…

Answer: WGCNA tutorial docs needed: Horvath Lab site down by Rebecca • 0

If there is a copy of the wgcna pdfs available please let me know!

Comment: How to filter .fasta file based on conditional statement by Brian Bushnell 19k

You're using BBTools v39.01. I just added the new flag in 39.06 :)

Answer: Where do these snpeff annotation come from? by Istvan Albert 99k

in principle you can do a snpeff dump hg38 that will generate a text output of the content of the database. in practice when I …

Comment: Can FPKM be used to create bar graphs for DEGs? by junli1988 • 0

LOL...It's a CSV file, and that's all I have in the folder. I agree that it is indeed the stuff of nightmares. But what can I do? It's not …

Answer: Is there a need to batch correct FPKM or TPM values for within sample comparison by jv ★ 1.2k

My assumption is that intra-sample comparisons should not require batch effect correction.

Comment: Tools or R / Python packages to perfom ML models by Michael 53k

If you have a lot of training data with class labels, as your dataset seems to be you could turn it into an ML classification problem. Gene…

Comment: p-value combination methods by Istvan Albert 99k

https://www.biostars.org/u/41501/ please don't delete post that have additional content associated with them having assistance from the C…

Comment: In what case there are RR reads but no LL reads when detect inversions using IGV by Istvan Albert 99k

I think a view as pairs is much cleaner as it shows the actual pairing and how they cross the gap. In the view you show it is not clear whe…

Answer: Extracting only soft/hard clipped reads from a bam file by Pierre Lindenbaum 158k

only soft clipped reads (but should be ok in most cases, as in bwa only secondary reads are hard clipped): samtools view -O BAM -o ou…

Comment: In what case there are RR reads but no LL reads when detect inversions using IGV by Jingfang • 0

Thanks for your reply. The IGV image I show used color alignments by pair orientation, and view mate region in split screen. Blue reads …

Answer: Extracting only soft/hard clipped reads from a bam file by horeyezonr ▴ 20

Hi I know it was more than a year, but I'll just leave the answer here maybe it will help someone. With the modified code of yours, th…

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