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Moderator: Asaf

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Asaf ♦ 4.1k
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Posts by Asaf

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Comment: C: trim adaptors RNA-seq
... I usually ignore over-represented sequences, especially in RNAseq. It depends a lot on the library preparation and in such low levels it's not a concern. You can test the FastQC on the R2 reads, they should have the same adapter sequence. run cutadapt as you intended (isn't it -a for forward and -A ...
written 8 days ago by Asaf ♦ 4.1k
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Comment: C: trim adaptors RNA-seq
... They do match. There is the initial A from the ligation and the end of the sequence you found is not present in the adapter sequence of FastQC. Go with the FastQC sequence ...
written 8 days ago by Asaf ♦ 4.1k
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Comment: C: change a mitochondria genome genebank file to a fasta file including multiple fa
... If you have the RefSeq accession number you can probably download it as a FASTA file ...
written 16 days ago by Asaf ♦ 4.1k
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Comment: C: RNA-seq compare FPKM's or fold change of different organisms
... Comparing read count between organisms is not recommended. Comparing fold-change, however, sounds like a good idea if you could find similar comparisons. ...
written 16 days ago by Asaf ♦ 4.1k
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Comment: C: Blastn: Blast short reads against genomes and retain only good hits
... you can add alignment length to output and filter according to it (using awk). ...
written 16 days ago by Asaf ♦ 4.1k
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Comment: C: Best way to address different batches of RNA-seq
... What was different between the two batches? In addition, as said above you shouldn't use RPKM, use statistics as in DESeq2 ...
written 11 weeks ago by Asaf ♦ 4.1k
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Answer: A: Gene abundance profile from metagenomics data
... I'm not aware of such a tool. You can try and classify your genes using interpro domains, MetaCyc/KEGG orthology groups etc. Depending on your depth of sequencing and sample complexity I would consider reference-based counting (i.e. mapping the reads to a reference using blastx) instead of assembly ...
written 11 weeks ago by Asaf ♦ 4.1k
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Comment: C: Normalization methods for metagenomics WGS data (not 16S data)
... DESeq2 normalization process assumes that most of the entities are the same in all of the samples. If you think that this assumption applies then you're good to go with DESeq2, you can go forward and do the entire analysis with it. If, however, this is not the case and the population is completely d ...
written 3 months ago by Asaf ♦ 4.1k
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Comment: C: Normalization methods for metagenomics WGS data (not 16S data)
... If you have a table with read counts then DESeq2 should work, the main issue here is what reference to use. ...
written 3 months ago by Asaf ♦ 4.1k
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Comment: C: Identifying paralogs using phylogenetic tree
... You might want to take a look at: https://www.nature.com/nature/journal/v449/n7158/full/nature06107.html They did this for fungi and were able to track down paralogs, especially after the whole genome duplication event. ...
written 3 months ago by Asaf ♦ 4.1k

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