User: jomo018

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jomo018420
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Posts by jomo018

<prev • 69 results • page 1 of 7 • next >
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Comment: C: Error using bedtools "intersect" command
... In addition to @finswimmer response, your sorting scheme is 1, 2, 3. If the gz file is chr1, chr2, chr3, it is probably sorted lexicographically (chr1, chr10). ...
written 18 hours ago by jomo018420
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Comment: C: Error using bedtools "intersect" command
... chromosomes on the bed file are: 1, 2, 3 rather than chr1, chr2, chr3? ...
written 18 hours ago by jomo018420
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Answer: A: Salmon (error: SAM file and fasta file have different transcript length)
... It seems that your transcript.fa contains the correct, 2237, length of this transcript. So the BAM file was incorrectly aligned. If you have the original fastq files, it may be better to use them directly with salmon. ...
written 2 days ago by jomo018420
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Comment: C: Salmon error message
... If you are worried about sra files, you can directly download your fastq.gz files here: [https://www.ebi.ac.uk/ena/data/view/SRR1056045][1] [1]: https://www.ebi.ac.uk/ena/data/view/SRR1056045 ...
written 3 days ago by jomo018420
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Answer: A: Fold change - a final explanation
... Fold change is **ratio** between values. Typically, the ratio is *final-to-inital* or *treated-to-control**. Log2, or % are just representations of the **ratio**. Log2 in partcular, usually reduces the "dynamic range" of the ratios in a monotonic mapping. So rather than handling ratios between 1-1 ...
written 4 days ago by jomo018420
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Answer: A: giving a color to null values on heatmap2
... You can use heatmap.2 *breaks* parameter to map between your 299 color shades and your fold-change values. Next assign NA to an "unused" figure (either larger than your maximum fold change or, in your case, possibly lower than your limit of 2). Finally, map this NA-figure to gray. In my experience, ...
written 17 days ago by jomo018420
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Comment: C: Illegal Division by zero
... That's not a good idea. $features[$oligo+1] does have a special meaning (summing *all* occurances). You should find out why it is zero, not replace it with something else. ...
written 27 days ago by jomo018420
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Comment: C: Illegal Division by zero
... They add *+1* to the **index** of *features*. It seems the *if* statement some 8 lines back is never true. ...
written 27 days ago by jomo018420
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Comment: C: How to append the cell barcode and UMI information to the fastq header in paired
... fastq.gz - is that two fastq files or one interleaved ? ...
written 4 weeks ago by jomo018420
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Comment: C: De-multiplex of no illumina index RNAseq libraries on Novaseq
... My humble recommendation, after several long unresolved discussions with sequencing guys is to search your internal barcode in both "undetermined" *and* G8. For 8 base codes, at a precise known location, error probability is low. ...
written 5 weeks ago by jomo018420

Latest awards to jomo018

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 6 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 7 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 7 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Why not merging?
Scholar 18 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?

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