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NCBI doesn't make our lives easy.
They want to make an interactive configuration about the sratoolkit
package: "sra-tools"
```
This sra toolkit installation has not been configured.
Before c…
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I thought I was missing some metadata in one of our own previously-submitted SRA datasets because it wasn't showing up in the CSV file, but then the SRA admins pointed out that it *does* show up on th…
ressy updated
5 years ago
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If we are downloading with keep_sra=false and sra_format as fastq it makes sence to check for fast files and do not download sra-s if fastq files are avaliable and forcerewrite = false
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- [x] optionally split left/right reads into seperate files for paired-end data in #762
- [ ] indicate that pileup files can become extremely large
- [x] support for multiple accession downloads - in…
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### Expected behavior
These data were identified by Nicolete (SigSci) Updates from Nicolette - https://docs.google.com/document/d/1uYqs939MU55D_3La8RUc8NJIYVrjLmVD-q_Tw5_Bjbg/edit
Viral DNA spike…
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I downloaded the Intel macos binaries for v2.5.1 (https://github.com/BenLangmead/bowtie2/releases/download/v2.5.1/bowtie2-2.5.1-macos-x86_64.zip) and tried to use the --sra-acc option like below:
…
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Error message I received:
$ aws s3 cp s3://logan-pub/c/SRR18385003/SRR18385003.contigs.fa.zst . --no-sign-request
fatal error: An error occurred (404) when calling the HeadObject operation: Key "c…
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Examples for ERR2756788.
Original summary header line [[S3 link](https://s3.amazonaws.com/lovelywater/summary/ERR2756788.summary)]:
```
SUMZER_COMMENT=sra=ERR2756788,genome=cov3ma,date=200607-0…
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- The database's entities should be renamed so that they follow proper db naming conventions
- This will help with readability for the columns on each table as well
- The following changes should be…
lohrd updated
4 years ago
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Hi, Leung,
I'm encountering an issue converting SRA files into BAM files with headers for subsequent analysis.
I've been using the following command to convert the raw SRA files into subreads BA…