Hi All,
Is there any way to use command line to download all unmapped.fq.bam only from MSBB RNA-seq? I do not need the mapped.bam files.
Thank you for your help in advance!
Li
Created by li chen lichenbiostat86 There are no limitations on publishing or using the data in support of grant applications. We only ask that you acknowledge the portal and data contributor. See here: https://adknowledgeportal.synapse.org/#/DataAccess/AcknowledgementStatements Thank you @Mette! I have another question, could we publish and release the intermediate results generated from the raw data? For example, can we publish gene expression values called from the raw RNA-seq data here? @lichenbiostat86 - there are 2 files per sample, a bam and a fastq with only the unmapped reads. The MSBB_RNAseq_covariates_November2018Update.csv lists both files for each sample with a few exceptions where the fastq entry is missing. This should not be an issue since the metadata information is the same for both file types Thank you @kelsey and @Mette ! I finally successfully download the unmapped fastq. However, I found there are only 1286 files compared to the metadata where contains 2559 files in the metadata file "MSBB_RNAseq_covariates_November2018Update.csv". Is there any way to download the complete 2559 file? Moreover, since I am the PI for the data request, can myself be both SIGNING OFFICIAL and PRINCIPAL INVESTIGATOR for the data request application? If not, who will be the ideal SIGNING OFFICIAL ?
`synTableQuery()` is sensitive to quotation.
Instead of using `synapser` to download fastq files, I recommend using the command line, as @Mette recommended. When you select the button **Download Options** to the right of the [table query](https://www.synapse.org/#!Synapse: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) , you can select **Programmatic Options**. You will see this command:
```
synapse get -q "SELECT * FROM syn11346063 WHERE ( ( \"study\" = 'MSBB' ) AND ( \"assay\" = 'rnaSeq' ) AND ( \"fileFormat\" = 'fastq' ) )"
```
See [these instructions](https://python-docs.synapse.org//build/html/CommandLineClient.html) to install the command line client. I did try
library(synapser)
library(synapserutils)
synLogin(email="lichen.emory@outlook.com", password="XXX")
results <- synTableQuery('SELECT * FROM syn11346063 WHERE ( ( study = "MSBB" ) AND ( assay = "rnaSeq" ) AND ( fileFormat = "fastq" ) )')
With error:
The error is Error in value[3L] : 400 Client Error:
Unknown column 'MSBB' in 'where clause'
programatic options do not target unmapped.fq and has error as well
files <- synapserutils::syncFromSynapse('syn11346063')
has error
Error in value[[3L]](cond) :
The provided id: syn11346063 is neither a container nor a File
You mean manually download one file by one file? There are 1000+ files and command line batch download is more realistic. Thank you! See Download options -> programatic options in the upper right of the table Thank you !
I tried .
results <- synTableQuery('SELECT * FROM syn11346063 WHERE ( ( study = "MSBB" ) AND ( assay = "rnaSeq" ) AND ( fileFormat = "fastq" ) )')
The error is Error in value[[3L]](cond) : 400 Client Error:
Unknown column 'MSBB' in 'where clause'
See this query of the file table: [SELECT * FROM syn11346063 WHERE ( ( "study" = 'MSBB' ) AND ( "assay" = 'rnaSeq' ) AND ( "fileFormat" = 'fastq' ) )](https://www.synapse.org/#!Synapse: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). That will get you the fastq only
Drop files to upload
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