Scdl Assignments 2013 Batch Files

Analyzing 454 Sequencing

General Steps

  1. Check Mapping File
  2. Split Library
  3. Pick OTUs
  4. Pick Representative Sequence
  5. Align (Optional to do now or after building the table)
  6. Assign Taxonomy
  7. Build OTU Table
  8. Align (if not performed before assigning the taxonomy table)

Notes

  • When running natively on MacQiime: must use macqiime (with a space after) before typing in code in the terminal window
    • macqiime check_id_map.py -m Fasting_Map.txt -o mapping_output -v
  • When running natively: $q/
    • $q/check_id_map.py -m Fasting_Map.txt -o mapping_output -v

Combine Data Sets

If you have two .fna and .qual files that you want to combine and you have the same barcodes for both data sets do the following:

  1. Combine .qual files (simple copy and paste into a new file)
  2. Combine .fna files
    1. First you must edit each .fna file
    • Copy and paste the file into Excel
    • It should show up with a title <G234 etc. followed by the sequences in the following cells
    • Ex. A1 = title A2 = sequence A3 = continuing sequence
    • In the next column type =IF(ISNUMBER(SEARCH(“*>*”,A1)),”G”,””)
    • This will put a G in the column B if column A has > (title)
    • Shift column B down 1 cell
    • In column C, =CONCATENATE(B1,A1)
    • This will add a letter at the beginning of each sequence
    • Save

Repeat with the second .fna file but be sure to use a different letter than G

Apply the same correction to the barcodes in your mapping files.

Creating Ordination Plot

  1. Align Sequences
  2. Filter
  3. Make Phylogenetic Tree
  4. Rarify

 

Analysis of beetle bacteria

  • checking the mapping file:: check_id_map.py -m Beetle_map_NEW.txt -o mapping_test
  • split_libraries.py -m Beetle_map_NEW.txt -f 5.TCA.454Reads.fna -q 5.TCA.454Reads.qual -o split_library_output
  • pick_otus.py -i seqs.fna -o picked_clustered_otus/ #kept at default: similarity 0.97; reverse strand matching did not change the output
  • picking representative sequences:: pick_rep_set.py -i picked_clustered_otus/seqs_otus.txt -f seqs.fna -o rep_set.fna #all default (the most common one)
  • alignment by MUSCLE:: align_seqs.py -i rep_set.fna -m muscle -o alignment/
  • taxonomy assignment:: assign_taxonomy.py -i rep_set.fna -m rdp
  • make_otu_table.py -i picked_clustered_otus/seqs_otus.txt -t rdp22_assigned_taxonomy/rep_set_tax_assignments.txt -o OTU_table_NEW.txt # making OTU table
  • rarefaction to three different levels: 41 (to get a few crassiusculus), 122 (to retain more mesonotal), 330.
    • example with 41: single_rarefaction.py -i OTU_table_NEW.txt -o rarefaction/rarefaction_41.txt -d 41
  • making preferences file:: make_prefs_file.py -m Beetle_map_NEW.txt -b”species,locality,species&&locality” -k white -o prefs_file.txt
  • make phylogeny using Fasttree:: make_phylogeny.py -i alignment/rep_set_aligned.fna -o rep_phylogeny.tre
  • beta diversity matrix of similarity
    • with full matrix: beta_diversity.py -i OTU_table_NEW.txt -t rep_phylogeny.tre -o b_diversity/
    • with rarefied matrices, e.g.: beta_diversity.py -i rarefaction/rarefaction_41.txt -t rep_phylogeny.tre -o b_diversity/
  • PCoA batch: principal_coordinates.py -i b_diversity/ -o PCoA/
  • making PCoA plots: make_2d_plots.py -i PCoA/pcoa_unweighted_unifrac_full_table.txt -m Beetle_map_NEW.txt -p prefs_file.txt -o 2d_plots/full_unweighted/
  • making UPGMA cluster: upgma_cluster.py -i b_divers_condensed/unweighted_unifrac_rarefaction_41.txt -o b_divers_condensed/UPGMA_output.txt
    • getting support for UPGMA nodes:
    • multiple rarefactions: multiple_rarefactions.py -i b_divers_condensed_batch/OTU_table_NEW_condensed.txt -o b_divers_condensed_batch/ -m 41 -x 330 -s 10 -n 2
    • beta_diversity.py -i b_divers_condensed_batch/ -t rep_phylogeny.tre -m unweighted_unifrac -o b_divers_condensed_batch_b_divers/
    • upgma_cluster.py -i b_divers_condensed_batch_b_divers/ -o b_divers_condensed_UPGMAs/
    • tree_compare.py -m b_diversity_condensed/master/UPGMA_master.tre -s b_divers_condensed_UPGMAs/ -o b_diversity_condensed/

WITH ZEROS for beetle without bacteria – didn’t work, the ones without bacteria drive all patterns

  • bray_curtis and Binary jaccard:: beta_diversity.py -i OTU_table_incl_zeros.txt -m bray_curtis,binary_jaccard -o b_diversity_incl_zeros/

#ashokedicherry

Hello everybody,can u help me to get the solved assignments of MBA HR 1st year in annamalai university.I just joint now in 2011 for this. anyone can help me ?
From Saudi Arabia, Mecca

#kush_call2

Dear Mr. Ashok, Greeting...!! could i have the details about annamalai university as i also wants to enroll in such course. i shall wait for your reply. Thanks
From India, Bharat

#simmraj

Dear all, Im new to this group, please provide me also the I year MBA (HR) Assignments as the last date of submission is 28 Feb.
From India, Kozhikode


#hrjoshi

3rd & 4th sem assignment of MBA HR SCDL, PUNE
Dear all,
I am a student of SCDL 2008 BATCH. please provide me 3rd & 4th sem assignment of MBA HR SCDL, PUNE. Its really urgent. I have these exam in april 1st week'2011
Personnel Administration
Industrial Relations and Labour Laws
TQM & HR
Organisational Development
Performance and Potential Management
Compensation Management
Strategic HR
Thanks & Regards:
Harsha
From India, New Delhi

#Suiee

Dear HR,
I joined late at annamalai university, so i was not able to submit the assignments withing the mentioned date(15.03.2012). i am going to write my exams in may 2013 and not in dec 2012.Can I submit the assignments for the same set of questions within march 2013? will they evaluate it?please help me
From India, Bangalore

#neethu harish

i have also the same problem ( i just missed the chance to file the assignment 2013 what is the next step i can do for the same annamalai university ) can i get the answer
also i need help to complete my assignment 2013 1st year HRM annamalai university.. please help me
From United Arab Emirates, Dubai

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