Moderator: swbarnes2
swbarnes2 ♦ 4.0k
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Posts by swbarnes2
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... 20 libraries So that's 7 trees, six tissues from each, with one of the pollen samples dropping out for some reason, right?
> However, I am not sure how to design the formula for DESeq2 since I
> only have two replicates for pollen.
That's not the problem. Your design is just "tissue". It' ...
written 5 hours ago by
swbarnes2 ♦ 4.0k
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... If you have removed reads because they did not map, or because they were duplicates, you do not need software to tell you that your bam file does not contain all the reads of the original fastq. ...
written 12 hours ago by
swbarnes2 ♦ 4.0k
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... In which case, converting it's format won't help. The poster in that case will need to use R, or a database program. But the poster almost certainly does not need to actually convert their file to .xlsx format. ...
written 1 day ago by
swbarnes2 ♦ 4.0k
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... Have you tried just opening the output in Excel? It's likely just tab delimited text, Excel shouldn't have an issue with that. Just pay attention to what Excel does to your gene names. ...
written 1 day ago by
swbarnes2 ♦ 4.0k
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107
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Answer:
A: discrepancy between reads
... > Im thinking about the homologous chromosome maybe doesn't have the
> deletion, or maybe DNA from multiple cells in one sample?
Either explanation could be the right one. It might be tricky to know which is correct. ...
written 1 day ago by
swbarnes2 ♦ 4.0k
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... Yes. It's perfectly possible, even if the reads are the same length. One might have sequences that are a little more repetitive, and therefore more compressible. If they have the same number of lines, that's all that matters.
It of course also possible to run gzip with different levels of compre ...
written 6 days ago by
swbarnes2 ♦ 4.0k
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... Are you trying to confirm that the fastq and bam are an exact match, or is spotchecking a few entries good enough? Would agreement in the # of reads be sufficient? ...
written 7 days ago by
swbarnes2 ♦ 4.0k
1
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109
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Answer:
A: STAR set --sjdbOverhang value
... You know the manual says about sjdbOverhang
> **In most cases, a generic value of 100 will work as well as the ideal**
> **value.**
http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STAR.posix/doc/STARmanual.pdf
...
written 8 days ago by
swbarnes2 ♦ 4.0k
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... If you want help, you need to provide images that help. You need to zoom in and show at least a dozen bases context on both sides of your problem. So your discrepancy is literally sitting on your reverse sanger primer? Did you use that reverse primer to do PCR prior to sanger sequencing? Does yo ...
written 8 days ago by
swbarnes2 ♦ 4.0k
2
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129
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1
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... I can't make heads or tails as to how your sanger data is supposed to correspond to your Illumina data. You need to zoom in on the region of interest, and show more flanking information.
Aside from the obvious possibility of sample mix-up, are there more than just those two SNPs? Does the Illumin ...
written 8 days ago by
swbarnes2 ♦ 4.0k
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