Hi All,
I want to download MSBB RNAseq data and I have two questions,
1) Is there any tool to download the raw fastq files for the MSBB RNAseq samples?
2) Where could I obtain the information regarding the control and AD sample information?
3) Where could I obtain the metadata information of the RNAseq data?
Created by li chen lichenbiostat86 In syn8612191, many of the samples are missing. Also, I have to say that fastq.gz files in syn7416949 have serious issues with the number of reads. If you convert Bam files to fastq files you can see that its better either to download Bam files and then convert them to fastq files or download files from syn8612191 but there many samples missing. Would you please check it and provide all the samples?
Thanks
Hi,
can you clarify about the 2entries: syn8612191 and syn7416949 ?
the syn8612191 entry contains files named *combined.fastq.gz but they only contain mapped reads ? Or is this an update where each file contains both mapped and unmapped reads ?
Can you confirm ? Thanks.
Unfortunately I don't believe so. You should be able to get all of the reads though by using picard to extract the mapped reads from the bams, and concatenate with the unmapped reads to get the full set of reads for each sample.
Ben Thanks, @ben.logsdon @jaeddy . Is there anyway we could obtain the original, unprocessed fastq files? We need to map the reads with our customized scripts. We truly appreciate your help! Those fastq files include both mapped and unmapped reads is my understanding. @jaeddy is this correct? We don't have original fastqs, we do have the bams and unmapped read fastqs though, which are here: syn7416949
Thanks,
Ben Hi Benjamin, thanks for helping. We are interested to explore some non coding RNA profiling with our own scripts, so is there anyway we could obtain the original, unprocessed RNAseq fastq files instead of mapped reads (accepted_hits)? We appreciate your help!
Best,
Bing Yao (Emory University) Hi Li Chen,
All of the fastq files for MSSM are here: syn8612191. Clinical data is here: syn6101474, rnaseq assay metadata is here: syn6100548. You can use the command line client and
```
synapse get -r syn8612191
```
To get all of the FASTQ files.
Best,
Ben