Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Minor
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Spring 8
Description
To ensure that the sequences are matching what we have versus what the SRA has, I came up with a simple check. We look for the first 10 sequences of a given SRA run across all the sequence files.
For speed, I head the fastq.gz file to get only the first 5 sequences.
Use zcat to keep files zipped.
Grep for the sequence of interest.
for f in *gz; do echo $f; zcat < $f | head -n 20 | grep "^CTGGCTTTTC" ; done
Probability dictates that we should find just 1 result.
Attachments
Issue Links
- blocks
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- Closed
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Activity
Testing one more:
RNA-Seq of Solanum lycopersicum:VF-36 pollen tube at 34C, 30 minutes, replicate 9 (SRR25478288)
First sequence is:
CTGGCTTTTCAGATTTCTCA
for f in *gz; do echo $f; zcat < $f | head | grep "^CTGGCTTTTCAGATTTCTC" ; done
V.34.30.7_R2.fastq.gz
V.34.30.8_R1.fastq.gz
V.34.30.8_R2.fastq.gz
V.34.30.9_R1.fastq.gz
CTGGCTTTTCAGATTTCTCATCCCTGTATGCTTTTCTTCGAGGTGGAGACACCTTCGGCACCTTGTCCACTACATCAGCTGAACTTTGCAAATTGGTTGTCGAGTACAGTTTCTGACCAGCTGGAATGCTGTACGCATTCTTCACCTCAA
V.34.30.9_R2.fastq.gz
V.34.45.7_R1.fastq.gz
V.34.45.7_R2.fastq.gz
Success!
Now one can go to SRA run selector:
Navigate to a sample, click the reads tab to see the first read.
Copy A portion of that read to grep all the files as mentioned above.
TTCATGAAGAGATCTCTTC
for f in *gz; do echo $f; zcat < $f | head | grep "^TTCATGAAGAGATCTCTTC" ; done
A.28.45.7_R1.fastq.gz
A.28.45.7_R2.fastq.gz
A.28.45.8_R1.fastq.gz
TTCATGAAGAGATCTCTTCTTTGTTGTGTCACCATTACCTCAATATTTGTTCCCTCCTTAGATTTTTGTTGAGAAGGAACAAATTCAACAATATAATCTGATACAGATAAAAGCCAGTTGATTTCTTTTTTCCATCTTGATTTTCTTTCT
A.28.45.8_R2.fastq.gz
A.28.45.9_R1.fastq.gz
A.28.45.9_R2.fastq.gz
(results above truncated to the part that matters.....)
It matches :
RNA-Seq of Solanum lycopersicum:anthocyanin reduced (are)pollen tube at 28C, 45 minutes, replicate 8 (SRR25478240)
Success.
When succesful, results will look a little like this
.....
V.28.45.9_R2.fastq.gz
V.28.75.7_R1.fastq.gz
V.28.75.7_R2.fastq.gz
V.28.75.8_R1.fastq.gz
V.28.75.8_R2.fastq.gz
V.28.75.9_R1.fastq.gz
V.28.75.9_R2.fastq.gz
V.34.15.7_R1.fastq.gz
V.34.15.7_R2.fastq.gz
V.34.15.8_R1.fastq.gz
V.34.15.8_R2.fastq.gz
V.34.15.9_R1.fastq.gz
V.34.15.9_R2.fastq.gz
V.34.30.7_R1.fastq.gz
V.34.30.7_R2.fastq.gz
V.34.30.8_R1.fastq.gz
V.34.30.8_R2.fastq.gz
V.34.30.9_R1.fastq.gz
CTGGCTTTTCAGATTTCTCATCCCTGTATGCTTTTCTTCGAGGTGGAGACACCTTCGGCACCTTGTCCACTACATCAGCTGAACTTTGCAAATTGGTTGTCGAGTACAGTTTCTGACCAGCTGGAATGCTGTACGCATTCTTCACCTCAA
V.34.30.9_R2.fastq.gz
V.34.45.7_R1.fastq.gz
V.34.45.7_R2.fastq.gz
V.34.45.8_R1.fastq.gz
V.34.45.8_R2.fastq.gz
V.34.45.9_R1.fastq.gz
V.34.45.9_R2.fastq.gz
V.34.75.7_R1.fastq.gz
V.34.75.7_R2.fastq.gz
V.34.75.8_R1.fastq.gz
V.34.75.8_R2.fastq.gz
V.34.75.9_R2.fastq.gz
We see just the 1 result and this matches the SRA title and ID for this sample. (and this is one of the 16 samples that got switched!!)
Will spot test a few more.
Nothing more to this. Moving to done and adding it to the archive.