Moderator: swbarnes2
swbarnes2 ♦ 4.5k
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Posts by swbarnes2
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... Why don't you read what the STAR manual says?
https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
> 2.2.1 Which chromosomes/scaffolds/patches to include? It is strongly recommended to include major chromosomes (e.g., for human
> chr1-22,chrX,chrY,chrM,) as well as un-placed and ...
written 4 hours ago by
swbarnes2 ♦ 4.5k
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... The submitters screwed up and didn't submit the second read. I checked to see if the submitters for some bizarre reason interleaved the two reads together in the one fastq file, but they didn't. If you want the whole data set, you'll have to contact the submitters directly. ...
written 8 days ago by
swbarnes2 ♦ 4.5k
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... The entry for this experiment in ENA agrees; paired data, just one read. Looking at the file, they didn't smuggle the data from read 2 in there anywhere, or interleave the reads together. ...
written 11 days ago by
swbarnes2 ♦ 4.5k
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... Those bam files were made by aligning to a list of transcripts. You cannot view them in IGV as aligned to chromsomes, but you can load the fasta of transcripts into IGV, and look at them by transcript. ...
written 11 days ago by
swbarnes2 ♦ 4.5k
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... That does not look like a count file, it looks like the header of a bam file, made by aligning a single sample to a fasta of short targets. It is not at all clear to me that that is the best way to align data for an experiment of this kind. But if you wanted counts, you could probably use samtools ...
written 11 days ago by
swbarnes2 ♦ 4.5k
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... If each patient is in only one batch, you cannot correct for both patient and batch. You cannot include both in your design. You might as well look at your samples with PCA, see how glaring the batch effect is. ...
written 11 days ago by
swbarnes2 ♦ 4.5k
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... Are you sure that your UMIs are in the read, and not in read 2? Why isn't the software 10xGenomics makes appropriate for what you are doing? ...
written 14 days ago by
swbarnes2 ♦ 4.5k
1
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1
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72
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1
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... Remember, DESeq's default library normalization is based on using the gene that has the median expression, and assuming that gene is expressed the same between all the samples. If you subset the genes differently, the median gene picked will be different. If you pick a curated set of 'interesting' ...
written 18 days ago by
swbarnes2 ♦ 4.5k
0
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... For starters, is the vcf the first intermediate file where the supercomputer results differ from the local PC?
And as Pierre says:
Software version differences are the likely answer, and `bwa samse | samtools sort` works fine, because samtools sort now works on sam files ...
written 19 days ago by
swbarnes2 ♦ 4.5k
1
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115
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... Since you have enough space, I wonder if the problem is that something is wrong with your output directory. Maybe its not being named properly? ...
written 19 days ago by
swbarnes2 ♦ 4.5k
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For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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For A: Blast: Homology Or Similarity?
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For C: how to identify a sequencing sample's gender
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For A: Is It Safe To Remove Exact Duplicate Reads In The Denovo Transcriptome Assembly?
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For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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