This data is ready for playing with.

2 new tasks are now possible given we have this data.

https://jira.bioviz.org/browse/IGBF-3645

https://jira.bioviz.org/browse/IGBF-3644

Review:

The md5 files seem to be the same. They don't contain much information besides names. I am not sure if there are other results that conclude the md5 check worked.

Time for Review!

I need review to go to HPC and go to this folder:

/projects/tomato_genome/rnaseq/30-986962648-Rasha-singleCell/00_fastq

Here we need to check that the files are in check via MD5sum.

You can check the 2 files originalmd5.txt and summarymd5.txt.
Make sure that they match.

It just so happens they have included an extra folder called S2.

In there is 1 file. 2_S1_L001_R2_001.fastq.gz

This MD5 is
6309aa304d0b17104ede19c1203df495 2_S1_L001_R2_001.fastq.gz

This is the correct one!!!!

I am moving this file so that they are all in the same folder.

The original MD5 sums reported by Azenta:
/projects/tomato_genome/rnaseq/30-986962648-Rasha-singleCell/00_fastq

1 line command to see all of the MD5
for file in *md5;do cat $file; done
8385565fbce53bbcc47eedc00e40a4ee ./1_S1_L001_I1_001.fastq.gz
253f30177f6ef940be21ce7344e0e1b7 ./1_S1_L001_I2_001.fastq.gz
864e999b8c444d477a0d68046da07210 ./1_S1_L001_R1_001.fastq.gz
5fdb505a254d522ed73887b8ad7bc135 ./1_S1_L001_R2_001.fastq.gz
116177f09c3b54526c002c6abb66710e ./2_S1_L001_I1_001.fastq.gz
f729927e6f889982d06de7fcf151d731 ./2_S1_L001_I2_001.fastq.gz
83f32c42be6ce90dc72691f4d84faa1d ./2_S1_L001_R1_001.fastq.gz
6309aa304d0b17104ede19c1203df495 ./2_S1_L001_R2_001.fastq.gz
fb47d7cfb8ef0ce389d6b74c693c1d8e ./3_S1_L001_I1_001.fastq.gz
88a091e3e5b31202cb57f5e97251e99f ./3_S1_L001_I2_001.fastq.gz
d37f458c2559c9c7da9f320efd9f040e ./3_S1_L001_R1_001.fastq.gz
6e95e26239fe076b42cf709b33a66493 ./3_S1_L001_R2_001.fastq.gz
a59b413031cf89ecc3c525a1bbcc7027 ./4_S1_L001_I1_001.fastq.gz
2df8c3a412d8df654f4aa4f1bcc7a0a2 ./4_S1_L001_I2_001.fastq.gz
e7def1b03b270c59107f92ee0b2a416c ./4_S1_L001_R1_001.fastq.gz
422d399ec511130cc15d0bf7c30c071f ./4_S1_L001_R2_001.fastq.gz

Next we run MD5 on each fastq file.
for file in *gz; do echo $file; md5sum $file >> summarymd5.txt; done

8385565fbce53bbcc47eedc00e40a4ee 1_S1_L001_I1_001.fastq.gz
253f30177f6ef940be21ce7344e0e1b7 1_S1_L001_I2_001.fastq.gz
864e999b8c444d477a0d68046da07210 1_S1_L001_R1_001.fastq.gz
5fdb505a254d522ed73887b8ad7bc135 1_S1_L001_R2_001.fastq.gz
116177f09c3b54526c002c6abb66710e 2_S1_L001_I1_001.fastq.gz
f729927e6f889982d06de7fcf151d731 2_S1_L001_I2_001.fastq.gz
83f32c42be6ce90dc72691f4d84faa1d 2_S1_L001_R1_001.fastq.gz
fb47d7cfb8ef0ce389d6b74c693c1d8e 3_S1_L001_I1_001.fastq.gz
88a091e3e5b31202cb57f5e97251e99f 3_S1_L001_I2_001.fastq.gz
d37f458c2559c9c7da9f320efd9f040e 3_S1_L001_R1_001.fastq.gz
6e95e26239fe076b42cf709b33a66493 3_S1_L001_R2_001.fastq.gz
a59b413031cf89ecc3c525a1bbcc7027 4_S1_L001_I1_001.fastq.gz
2df8c3a412d8df654f4aa4f1bcc7a0a2 4_S1_L001_I2_001.fastq.gz
e7def1b03b270c59107f92ee0b2a416c 4_S1_L001_R1_001.fastq.gz
422d399ec511130cc15d0bf7c30c071f 4_S1_L001_R2_001.fastq.gz

Step 3 we compare the hashes:
awk '

' summarymd5.txt > tmpnew
diff tmporig tmpnew

They are all the same but one!!!

6309aa304d0b17104ede19c1203df495 ./2_S1_L001_R2_001.fastq.gz