Difference between revisions of "JP Feb 16 16"

Latest revision as of 19:57, 16 February 2016

Wrote a Media:Renamer.txt python document to rename the raw fastq files.

Go to Terminal. Go into your destination file. cp -r ../campbell/fastQCintestine/trim_#i.fastq #destination_file_name

Ran Blast2Go using NCBI database and the following parameters (default):

Blast2GO on the first 20 genes from small intestine trimmed 1: The blast search took 3 minutes for 20 sequences on 20-results output.

Press "mapping" Press "annotate"

We then ran 250

@@ Line 1: / Line 1: @@
 [[Julia Preziosi]]
-Wrote a python code to rename the raw fastq files. (at bottom of page)
+Wrote a [[Media:Renamer.txt]] python document to rename the raw fastq files.
-Ran Blast2Go using NCBI database and the following parameters (default):
+Go to Terminal.
+Go into your destination file.
+cp -r ../campbell/fastQCintestine/trim_#i.fastq #destination_file_name
+Ran Blast2Go using NCBI database and the following parameters (default):
+[[File:default1.png]]
+[[File:default2.png]]
+Blast2GO on the first 20 genes from small intestine trimmed 1:
+The blast search took 3 minutes for 20 sequences on 20-results output.
+[[File:blast2go20.png]]
+Press "mapping"
+Press "annotate"
-#file_name = raw_input('Enter file name: ').strip()
+We then ran 250
-file_name = 'first80.txt'
-Seqlist= []
-f = open(file_name)
-for pos, line in enumerate(f):
-    if pos % 4 == 1:
-        Seqlist.append(line)
-f.close()
-NewSeqlist = []
-ID = 1
-for seq in Seqlist:
-    seq = ">" + str(ID) + "\n" + seq
-    NewSeqlist.append(seq)
-    ID += 1
-print NewSeqlist
-newfilename = "renamed_" + file_name
-with open (newfilename, 'w') as newfile:
-    for seq in NewSeqlist:
-        newfile.write(seq)