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Recent Replies
Answer: b37 liftover
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Giulio Genovese
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Using [BCFtools/liftover](https://doi.org/10.1093/bioinformatics/btae038) will automatically take care of:
- flexible contig names (e.g. …
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Please copy and paste the actual code instead of posting screenshots. You can format the text as `code` by using `101010` button in edit wi…
Answer: Strange offsetting in deeptools?
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It does seem like you want to set offset as 1 to return the first base of your read.
Have you done something to try and remove read2? T…
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those are GVCF files, not standard VCF files, you cannot merge those files without using the INFO column.
Comment: Merging gvcf files between Dragen and other calling tools
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Did you not merge them all then or just rid of the INFO entirely?
Many thanks!
Comment: Merging gvcf files between Dragen and other calling tools
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Hi tried to use GATK CombineGVCFs a while ago, without success, the INFO are not compatible.
Comment: Issue with CIBERSORTx Error 139
by
Hamdache
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0
Thanks for your help I will keep you updated
Comment: Download SRA raw data using efetch
by
biofysikos
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Thank you @genomax! It all makes sense (for now).
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If you are able to resolve the name of the resource by doing `host cibersortx.stanford.edu` then it is possible that the method/API you are…
Comment: Download SRA raw data using efetch
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> I can just use curl to download the URL extracted by efetch
As long as you are aware of the limitations (e.g. there may be a single file…
Comment: Issue with CIBERSORTx Error 139
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Hamdache
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Apparently yes I tried ping -c 4 google.com
ping -c 4 google.com
PING google.com (142.251.37.174) 56(84) bytes of data.
64 by…
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While someone will be along with an answer that is specific based on their experience you may want to try asking ChatGPT these two question…
Comment: Download SRA raw data using efetch
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Thank you @genomax . So to recapitulate, I can just use `curl` to download the URL extracted by `efetch`.
When you say ENA, do you mean th…
Comment: Issue with CIBERSORTx Error 139
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GenoMax
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> Failed to get address info of cibersortx.stanford.edu: Resource temporarily unavailable
Does your docker container have access to intern…
Comment: Issue with CIBERSORTx Error 139
by
Hamdache
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Thank you for your response. The issue occurred while executing the following function in R:
computeCBSX = function(TPM_matrix, signa…
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