Hi,
Salvatore said there is bam file in https://nfhack-platform.bemyapp.com/#/insights/5f6c16e1a81cb3001b005a00.
Jineta said take a look at Step 3 in this link :https://www.synapse.org/#!Synapse:syn22336443/wiki/605246 for access to RNAseq data available for the hackathon.
However, I read all about the Data, and run it in R. I did not find the RNA sequence bam file. Our Methods are working on the bam file. Could you send me more details on how to get the bam format file?
Thank you.
Created by Xuye Luo luoxuye Hi @luoxuye ,
The best way to look for available bam files is on the NF Data Portal. You can [use this link to view all publicly available bam files](https://nf.synapse.org/Explore/Files?QueryWrapper0=%7B%22sql%22%3A%22SELECT%20id%20AS%20%5C%22File%20ID%5C%22%2C%20assay%2C%20dataType%2C%20diagnosis%2C%20tumorType%2C%20%20species%2C%20individualID%2C%20%20fileFormat%2C%20dataSubtype%2C%20nf1Genotype%20as%20%5C%22NF1%20Genotype%5C%22%2C%20nf2Genotype%20as%20%5C%22NF2%20Genotype%5C%22%2C%20studyName%2C%20fundingAgency%2C%20consortium%2C%20name%20AS%20%5C%22File%20Name%5C%22%2C%20accessType%2C%20accessTeam%20%20FROM%20syn16858331%20WHERE%20resourceType%20%3D%20%27experimentalData%27%22%2C%22limit%22%3A25%2C%22offset%22%3A0%2C%22selectedFacets%22%3A%5B%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22assay%22%2C%22facetValues%22%3A%5B%22rnaSeq%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22dataType%22%2C%22facetValues%22%3A%5B%22geneExpression%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22accessType%22%2C%22facetValues%22%3A%5B%22PUBLIC%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22fileFormat%22%2C%22facetValues%22%3A%5B%22bam%22%5D%7D%5D%7D)
To access the original files of the datasets mentioned in Step 3 of the Genomics data section, you can follow the links given below.
Please note that 1) Not all investigators have uploaded bam files which is why we have made the counts table available for the participant's convenience, 2) Some contributors have not given access to the original files, so you may have to specifically ask them for access to the original files.
cnf_data_resource: https://www.synapse.org/#!Synapse:syn7979306
synodos_nf2 : https://www.synapse.org/#!Synapse:syn10881683, https://www.synapse.org/#!Synapse:syn18456447
synodos_nf1 : https://www.synapse.org/#!Synapse:syn5643678
jhu_biobank : https://www.synapse.org/#!Synapse:syn19522967
nf1_glioma : https://www.synapse.org/#!Synapse:syn8466642
pnf_cell_line : https://www.synapse.org/#!Synapse:syn18468125, https://www.synapse.org/#!Synapse:syn9928390
wustl : https://www.synapse.org/#!Synapse:syn12851064
Hope this helps,
Jineta