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New samples #21

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merged 18 commits into from
Mar 30, 2018
Merged

New samples #21

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0453518
added three more samples
aortiz24 Jul 20, 2017
a30e68d
uncommented lines 16-19
aortiz24 Jul 20, 2017
0d22a68
remove SRP018247.lst from data directory
aortiz24 Jul 20, 2017
8cc3306
move SRP018247.lst to data directory
aortiz24 Jul 20, 2017
bba762e
updated file
aortiz24 Jul 20, 2017
527e64f
added needed directory
aortiz24 Jul 20, 2017
c4d0b78
Revert "added needed directory"
aortiz24 Jul 22, 2017
1c27544
Local directory behind 1 commit, need to pull from remote directory
aortiz24 Jul 22, 2017
61316bc
updated code for lines 39, 45,48
aortiz24 Jul 22, 2017
512f1ea
Merge https://github.com/k8hertweck/FieldLabComparison into New_samples
aortiz24 Aug 2, 2017
76b50a4
added necessary dash in line 39
aortiz24 Aug 15, 2017
70b1c6a
added new samples to data preparation script
aortiz24 Aug 15, 2017
7ba34ee
added hashtag to line 18
aortiz24 Aug 15, 2017
4cd441d
added name to merge.files command output file
aortiz24 Aug 15, 2017
f1bd9af
added functioning code
aortiz24 Aug 15, 2017
60d17f6
Merge branch 'master' into New_samples
k8hertweck Mar 29, 2018
0263b9a
adding EOF line
k8hertweck Mar 29, 2018
d1e691a
correcting lab/field assignment
k8hertweck Mar 30, 2018
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3 changes: 3 additions & 0 deletions data/SRP018247.lst
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Original file line number Diff line number Diff line change
@@ -1,3 +1,6 @@
SRR655969
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Why did you include these three samples in the list? They're excluded from the analysis, so it's not clear why we'd need to have them downloaded, etc.

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OK, I see what happened: the numbers aren't sorted from the original sheet, and you've added them in duplicate. I'll take care of this.

SRR655970
SRR655971
SRR655972
SRR655973
SRR655974
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20 changes: 10 additions & 10 deletions mothur_prep.sh
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Expand Up @@ -13,10 +13,10 @@ for x in `cat SRP018246.lst`
do
mothur "#fastq.info(fastq=SRP018246/$x.fastq)"
done
#for x in `cat SRP018247.lst`
# do
# mothur "fastq.info(fastq=SRP018247/$x.fastq)"
#done
for x in `cat SRP018247.lst`
do
mothur "#fastq.info(fastq=SRP018247/$x.fastq)"
done

rm *.logfile

Expand All @@ -36,15 +36,15 @@ done

# create group file
# output mergegroups
mothur "#make.group(fasta=SRR655327.trim.fasta-SRR655328.trim.fasta-SRR655329.trim.fasta-SRR655330.trim.fasta-SRR655331.trim.fasta-SRR655332.trim.fasta-SRR655333.trim.fasta-SRR655334.trim.fasta-SRR655335.trim.fasta-SRR655336.trim.fasta-SRR655337.trim.fasta-SRR655338.trim.fasta-SRR655339.trim.fasta-SRR655340.trim.fasta-SRR655341.trim.fasta-SRR655342.trim.fasta-SRR655343.trim.fasta-SRR655344.trim.fasta-SRR655345.trim.fasta-SRR655346.trim.fasta-SRR655347.trim.fasta-SRR655348.trim.fasta-SRR655349.trim.fasta-SRR655350.trim.fasta-SRR655351.trim.fasta-SRR655352.trim.fasta-SRR655353.trim.fasta-SRR655354.trim.fasta-SRR655355.trim.fasta-SRR655356.trim.fasta-SRR655357.trim.fasta-SRR655358.trim.fasta-SRR655359.trim.fasta-SRR655360.trim.fasta-SRR655361.trim.fasta-SRR655362.trim.fasta-SRR655363.trim.fasta-SRR655364.trim.fasta, groups=field-field-field-field-lab-lab-lab-lab-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-lab-lab-lab-lab-field-field-field-field)"
mothur "#make.group(fasta=SRR655327.trim.fasta-SRR655328.trim.fasta-SRR655329.trim.fasta-SRR655330.trim.fasta-SRR655331.trim.fasta-SRR655332.trim.fasta-SRR655333.trim.fasta-SRR655334.trim.fasta-SRR655335.trim.fasta-SRR655336.trim.fasta-SRR655337.trim.fasta-SRR655338.trim.fasta-SRR655339.trim.fasta-SRR655340.trim.fasta-SRR655341.trim.fasta-SRR655342.trim.fasta-SRR655343.trim.fasta-SRR655344.trim.fasta-SRR655345.trim.fasta-SRR655346.trim.fasta-SRR655347.trim.fasta-SRR655348.trim.fasta-SRR655349.trim.fasta-SRR655350.trim.fasta-SRR655351.trim.fasta-SRR655352.trim.fasta-SRR655353.trim.fasta-SRR655354.trim.fasta-SRR655355.trim.fasta-SRR655356.trim.fasta-SRR655357.trim.fasta-SRR655358.trim.fasta-SRR655359.trim.fasta-SRR655360.trim.fasta-SRR655361.trim.fasta-SRR655362.trim.fasta-SRR655363.trim.fasta-SRR655364.trim.fasta-SRR655990.trim.fasta-SRR655991.trim.fasta-SRR655992.trim.fasta-SRR655993.trim.fasta-SRR655994.trim.fasta-SRR655995.trim.fasta-SRR655996.trim.fasta-SRR655997.trim.fasta-SRR655998.trim.fasta-SRR655999.trim.fasta-SRR656000.trim.fasta-SRR656001.trim.fasta-SRR656002.trim.fasta-SRR656003.trim.fasta-SRR656004.trim.fasta-SRR656005.trim.fasta-SRR656006.trim.fasta-SRR656022.trim.fasta-SRR656023.trim.fasta-SRR656024.trim.fasta-SRR656025.trim.fasta-SRR656026.trim.fasta-SRR656027.trim.fasta-SRR656028.trim.fasta-SRR656029.trim.fasta-SRR656030.trim.fasta-SRR656031.trim.fasta-SRR656032.trim.fasta-SRR656033.trim.fasta, groups=field-field-field-field-lab-lab-lab-lab-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-lab-lab-lab-lab-field-field-field-field-field-field-field-field-field-field-field-field-field-lab-lab-lab-field-field-field-field-field-field-field-field-field-field-field-field-field-lab-field-field-field)"

# rename groups file
cp mergegroups analysis.groups

# make master fasta file (combines individual fasta files into a single file, analysis.fasta)
mothur "#merge.files(input=SRR655327.trim.fasta-SRR655328.trim.fasta-SRR655329.trim.fasta-SRR655330.trim.fasta-SRR655331.trim.fasta-SRR655332.trim.fasta-SRR655333.trim.fasta-SRR655334.trim.fasta-SRR655335.trim.fasta-SRR655336.trim.fasta-SRR655337.trim.fasta-SRR655338.trim.fasta-SRR655339.trim.fasta-SRR655340.trim.fasta-SRR655341.trim.fasta-SRR655342.trim.fasta-SRR655343.trim.fasta-SRR655344.trim.fasta-SRR655345.trim.fasta-SRR655346.trim.fasta-SRR655347.trim.fasta-SRR655348.trim.fasta-SRR655349.trim.fasta-SRR655350.trim.fasta-SRR655351.trim.fasta-SRR655352.trim.fasta-SRR655353.trim.fasta-SRR655354.trim.fasta-SRR655355.trim.fasta-SRR655356.trim.fasta-SRR655357.trim.fasta-SRR655358.trim.fasta-SRR655359.trim.fasta-SRR655360.trim.fasta-SRR655361.trim.fasta-SRR655362.trim.fasta-SRR655363.trim.fasta-SRR655364.trim.fasta, output=analysis.trim.fasta)"
# make master fasta file (combines individual fasta files into a single file, analysis.trim.fasta)
mothur "#merge.files(input=SRR655327.trim.fasta-SRR655328.trim.fasta-SRR655329.trim.fasta-SRR655330.trim.fasta-SRR655331.trim.fasta-SRR655332.trim.fasta-SRR655333.trim.fasta-SRR655334.trim.fasta-SRR655335.trim.fasta-SRR655336.trim.fasta-SRR655337.trim.fasta-SRR655338.trim.fasta-SRR655339.trim.fasta-SRR655340.trim.fasta-SRR655341.trim.fasta-SRR655342.trim.fasta-SRR655343.trim.fasta-SRR655344.trim.fasta-SRR655345.trim.fasta-SRR655346.trim.fasta-SRR655347.trim.fasta-SRR655348.trim.fasta-SRR655349.trim.fasta-SRR655350.trim.fasta-SRR655351.trim.fasta-SRR655352.trim.fasta-SRR655353.trim.fasta-SRR655354.trim.fasta-SRR655355.trim.fasta-SRR655356.trim.fasta-SRR655357.trim.fasta-SRR655358.trim.fasta-SRR655359.trim.fasta-SRR655360.trim.fasta-SRR655361.trim.fasta-SRR655362.trim.fasta-SRR655363.trim.fasta-SRR655364.trim.fasta-SRR655990.trim.fasta-SRR655991.trim.fasta-SRR655992.trim.fasta-SRR655993.trim.fasta-SRR655994.trim.fasta-SRR655995.trim.fasta-SRR655996.trim.fasta-SRR655997.trim.fasta-SRR655998.trim.fasta-SRR655999.trim.fasta-SRR656000.trim.fasta-SRR656001.trim.fasta-SRR656002.trim.fasta-SRR656003.trim.fasta-SRR656004.trim.fasta-SRR656005.trim.fasta-SRR656006.trim.fasta-SRR656022.trim.fasta-SRR656023.trim.fasta-SRR656024.trim.fasta-SRR656025.trim.fasta-SRR656026.trim.fasta-SRR656027.trim.fasta-SRR656028.trim.fasta-SRR656029.trim.fasta-SRR656030.trim.fasta-SRR656031.trim.fasta-SRR656032.trim.fasta-SRR656033.trim.fasta, output=analysis.trim.fasta)"

# make master qual file
mothur "#merge.files(input=SRR655327.trim.qual-SRR655328.trim.qual-SRR655329.trim.qual-SRR655330.trim.qual-SRR655331.trim.qual-SRR655332.trim.qual-SRR655333.trim.qual-SRR655334.trim.qual-SRR655335.trim.qual-SRR655336.trim.qual-SRR655337.trim.qual-SRR655338.trim.qual-SRR655339.trim.qual-SRR655340.trim.qual-SRR655341.trim.qual-SRR655342.trim.qual-SRR655343.trim.qual-SRR655344.trim.qual-SRR655345.trim.qual-SRR655346.trim.qual-SRR655347.trim.qual-SRR655348.trim.qual-SRR655349.trim.qual-SRR655350.trim.qual-SRR655351.trim.qual-SRR655352.trim.qual-SRR655353.trim.qual-SRR655354.trim.qual-SRR655355.trim.qual-SRR655356.trim.qual-SRR655357.trim.qual-SRR655358.trim.qual-SRR655359.trim.qual-SRR655360.trim.qual-SRR655361.trim.qual-SRR655362.trim.qual-SRR655363.trim.qual-SRR655364.trim.qual, output=analysis.trim.qual)"
# make master qual file, analysis.trim.qual
mothur "#merge.files(input=SRR655327.trim.qual-SRR655328.trim.qual-SRR655329.trim.qual-SRR655330.trim.qual-SRR655331.trim.qual-SRR655332.trim.qual-SRR655333.trim.qual-SRR655334.trim.qual-SRR655335.trim.qual-SRR655336.trim.qual-SRR655337.trim.qual-SRR655338.trim.qual-SRR655339.trim.qual-SRR655340.trim.qual-SRR655341.trim.qual-SRR655342.trim.qual-SRR655343.trim.qual-SRR655344.trim.qual-SRR655345.trim.qual-SRR655346.trim.qual-SRR655347.trim.qual-SRR655348.trim.qual-SRR655349.trim.qual-SRR655350.trim.qual-SRR655351.trim.qual-SRR655352.trim.qual-SRR655353.trim.qual-SRR655354.trim.qual-SRR655355.trim.qual-SRR655356.trim.qual-SRR655357.trim.qual-SRR655358.trim.qual-SRR655359.trim.qual-SRR655360.trim.qual-SRR655361.trim.qual-SRR655362.trim.qual-SRR655363.trim.qual-SRR655364.trim.qual-SRR655990.trim.qual-SRR655991.trim.qual-SRR655992.trim.qual-SRR655993.trim.qual-SRR655994.trim.qual-SRR655995.trim.qual-SRR655996.trim.qual-SRR655997.trim.qual-SRR655998.trim.qual-SRR655999.trim.qual-SRR656000.trim.qual-SRR656001.trim.qual-SRR656002.trim.qual-SRR656003.trim.qual-SRR656004.trim.qual-SRR656005.trim.qual-SRR656006.trim.qual-SRR656022.trim.qual-SRR656023.trim.qual-SRR656024.trim.qual-SRR656025.trim.qual-SRR656026.trim.qual-SRR656027.trim.qual-SRR656028.trim.qual-SRR656029.trim.qual-SRR656030.trim.qual-SRR656031.trim.qual-SRR656032.trim.qual-SRR656033.trim.qual, output=analysis.trim.qual)"

rm *.logfile
rm *.logfile