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Hi, golharam and simonandrews
Thanks! I am using WinXP. I will try to run SeqMonk on my desktop first to see if it works.
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Thanks! I am using WinXP. I will try to run SeqMonk on my desktop first to see if it works.
-c
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This week I discovered that using BigWig files for coverage data works really nicely in GBrowse.
I would really love to have a simple plotting tool to take per chromosome coverage data from something like a BigWig file and plot a nice looking coverage figure. I'm thinking of coding it myself in (probably) python or (maybe) R but if anyone can point me to examples to get started that would be great. Although some genome browsers make coverage plots, they just don't look nice for publication use IMHO.Last edited by natstreet; 10-01-2010, 08:10 AM.Comment
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Hi, simonandrews
I just noticed that the SeqMonk Release Notes talks about SeqMonk v0.12.0 but it seems I can only find SeqMonk v0.11.0 online. Do you know where to find v0.12.0?
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I can see v0.11.0 listed at their website and if you swap 11 to 12 in the download URL there is something there to be downloaded
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Sorry, I'd failed to copy over the new version of the download page from our staging server. If you try again now the links should be in place (if you don't see them press shift+refresh in your browser to force a cache update).Originally posted by cliff View Post
Simon.Comment
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IGV scripting function
Use IGV to output plots of a region of a bam file with the following sample script
attached is an example (note path to bam and snapshotDirectory need to be absolute not relative)
new
load myfile.bam
snapshotDirectory mySnapshotDirectory
genome hg18
goto chr1:65,289,335-65,309,335
sort position
collapse
snapshotComment
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<shameless plug>Originally posted by arnoldliao View PostUse IGV to output plots of a region of a bam file with the following sample script
attached is an example (note path to bam and snapshotDirectory need to be absolute not relative)
new
load myfile.bam
snapshotDirectory mySnapshotDirectory
genome hg18
goto chr1:65,289,335-65,309,335
sort position
collapse
snapshot
Note that BEDTools has a tool called bedToIGV that will automatically create an IGV batch script from a BED, GFF, or VCF file.
</shameless plug>Comment
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Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM -
Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...07-08-2026, 05:17 AM -
Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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