How to match tumor fastq file to normal fastq file? (I just have a set of tumor data and another set of normal data)
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7 weeks ago
Joshua • 0

Hi,

I have downloaded two sets of fastq files from SRA database. PRJNA421846 (set1) contains Whole Exome Sequencing of tumor dataset form 96 patients (There are totally 154 fastq files few are pre-therapy, few are during-therapy, and remaining are post-therapy). PRJNA427604 (set2) contains matched normal for 40 patients.

However, these data are not matched. (i.e) I'm not able to find out which of these 40 normal fastq files matches with 154 tumor data.

I need the data in the following format for my analysis :

Patient1 - tumor fastq file; normal fastq file

Patient2 - tumor fastq file; nomral fastq file

.

.

.

Patient40 - tumor fastq file; nomral fastq file

Tumor set: https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA421846

Normal set: https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA427604

Is there any way to figure out which of these sets matches with eachother?

WholeExomeSequencing NextGenerationSequencing • 184 views
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Entering edit mode
7 weeks ago
tomas4482 ▴ 340

Check SRA selector runner for metadata, GEOdataset for metadata, original article for sampling tables or ask the authors. This is not a technical issue so there is little we can do to help

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