Moderator: Damian Kao
Damian Kao ♦ 15k
- Reputation:
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- http://blog.nextgeneti...
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- Joined:
- 7 years ago
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Bioinformatician at Janelia Research Campus.
Posts by Damian Kao
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... As with most interval operations, bedtools has a command for it:
https://bedtools.readthedocs.io/en/latest/content/tools/flank.html ...
written 16 days ago by
Damian Kao ♦ 15k
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Comment:
C: SNP calling from BAM file
... Can you please post the command you used and the error message. ...
written 28 days ago by
Damian Kao ♦ 15k
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252
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... Packages like edgeR and DESeq2 don't actually transform the counts for DE analysis. A normalization factor is calculated and then used in the DE test. There are good information in the absolute counts for each gene. Standardization is not used, otherwise that information would be lost. ...
written 6 weeks ago by
Damian Kao ♦ 15k
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Comment:
C: Abyss run time
... What's the estimated genome size of your organism? And how many reads do you have? ...
written 6 weeks ago by
Damian Kao ♦ 15k
1
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... I think the problem you have with SNPGenie might not be related to CDS length not being a multiple of 3. What is the exact error message you get from SNPGenie?
In the SNPGenie usage instructions: https://github.com/chasewnelson/SNPGenie
It says that it reads the gene_id field to concatenate CDS li ...
written 6 weeks ago by
Damian Kao ♦ 15k
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... Yes, it is true that CDS features in a gtf/gff file are broken up into multiple intervals when the gene is multi-exonic.
Gene/Transcript features describe the entire gene from start of 5\` UTR to end of 3\` UTR. Exon features describe multiple exon intervals, including 5\`/3\` UTRs. CDS describes ...
written 7 weeks ago by
Damian Kao ♦ 15k
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... There are potentially multiple CDS lines for each transcript in a .gtf file. Each CDS line define an interval that correspond to multiple exons. The length of each CDS line does not have to be in a multiple of three. But the sum length of multiple CDS lines for each transcript should be in a multipl ...
written 7 weeks ago by
Damian Kao ♦ 15k
1
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... So you have 88 sets of metagenomic reads? I don't see why not just merge them all and treat them as one huge metagenomic read set and assemble that with metagenome aware assembler (metaSpades or something). And from the resulting assembly, pull out the contigs you want based on reference mapping. ...
written 7 weeks ago by
Damian Kao ♦ 15k
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... I would suggest using a newer version of Trinity. You are using a 2011 version. There has been a lot of new development since then that might fix your issue. ...
written 7 weeks ago by
Damian Kao ♦ 15k
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... The .gff file you downloaded doesn't describe gene annotations. It just describes the genome scaffolds/contigs. There doesn't appear to be any gene annotations in the NCBI ftp you posted.
You do not need to provide StringTie with a set of reference annotations. You can perform an assembly just wit ...
written 7 weeks ago by
Damian Kao ♦ 15k
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For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
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For A: A Farewell To Bioinformatics
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