Moderator: swbarnes2

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swbarnes24.5k
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Posts by swbarnes2

<prev • 497 results • page 1 of 50 • next >
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Answer: A: Genome index and Aligment with STAR- Rattus Norvegicus
... 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 swbarnes24.5k
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Answer: A: Problem: "Pair-end" reads scRNA seq data (Drop-seq)
... 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 swbarnes24.5k
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Answer: A: Paired-End Data Only Has One Read Per Spot
... 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 swbarnes24.5k
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Answer: A: How to load BAM files that do not have chromosome name in the header?
... 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 swbarnes24.5k
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Answer: A: Differential expression analysis on miRNA count files
... 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 swbarnes24.5k
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Answer: A: Batch effect correction - miRNA sequencing - DESeq2
... 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 swbarnes24.5k
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Comment: C: split BAM file with same cell-barcode and UMI pair
... 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 swbarnes24.5k
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Comment: C: Deseq2 - Log2FoldChange is dependent on the number of genes in the analysis
... 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 swbarnes24.5k
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Answer: A: Difference in output VCF between running on a local PC and supercomputer cluster
... 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 swbarnes24.5k
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Comment: C: Rsubread: ERROR: cannot finish the SAM file
... 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 swbarnes24.5k

Latest awards to swbarnes2

Teacher 11 days ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 5 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 5 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 9 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 9 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Blast: Homology Or Similarity?
Scholar 4 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: how to identify a sequencing sample's gender
Scholar 6 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 6 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 6 months ago, created an answer that has been accepted. For A: Problem with FPKM values
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Scholar 8 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 8 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 8 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 8 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 9 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 9 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 10 months ago, created an answer that has been accepted. For A: Problem with FPKM values

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