User: jaqx008
jaqx008 • 10
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Posts by jaqx008
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Comment:
C: Mapping with Fasta vs fastq
... Oh. My bad. I guess I just read the body of the message. Thanks again ...
written 3 days ago by
jaqx008 • 10
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Comment:
C: Mapping with Fasta vs fastq
... I just found out that I needed to specify -f so bowtie could recognize the fasta and that worked.
Thanks for your contribution ...
written 3 days ago by
jaqx008 • 10
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Comment:
C: Mapping with Fasta vs fastq
... Bellow is the command I just tried and it yielded a zero byte file.
bowtie .fasta --un Amph.unmapped.pi.fasta --al Amph.mapped.pi.fasta -S male.mappedfasta.sam ...
written 4 days ago by
jaqx008 • 10
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... Hey Everyone, I am trying to map small RNAs to a genome using Bowtie1. I initially did this with the following command and with a fastq file. But this time i want to use a fasta file and don't know if the command should change or remain the same. I tried and it didn't work though. The bowtie -h is n ...
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... Oh Ok. Will read it. but it sounds good for the python version ...
written 7 days ago by
jaqx008 • 10
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... I understand now. It worked. Thanks so much. It ran and gave me the output. Thanks Bastien ...
written 7 days ago by
jaqx008 • 10
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... I am just going to try now. Does that mean i Should edit the script and replace
genomicKey in self.alignement_dic.keys(): with
genomicKey in list(self.alignement_dic):?
I don't understand
...
written 7 days ago by
jaqx008 • 10
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... more from around line 77
coord = read.reference_start
pol = 'F'
dic[(chrom, coord, pol)].append(read.query_sequence)
for key in dic:
dic[key] = set(dic[key])
return dic
def query_positions(self, bam_object, overlap):
...
written 7 days ago by
jaqx008 • 10
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... python version is Python 3.6.3. overlap.py code is bellow. I have tried to down grade the python but the 3.6.3 still shows in my terminal. couldn't paste the entire code because of the number of characters. this is only part of the code.
import argparse
from collections import defaultdict
...
written 7 days ago by
jaqx008 • 10
• updated
7 days ago by
Devon Ryan ♦ 78k
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... Hello all. I ran into this error and have been trying to fix it with numerous online suggestions but non really worked.
I am trying to use a python script to find siRNA overlap in my alignment file. But I keep getting the following error. some of the languages to fix it from online suggestions seem ...
written 7 days ago by
jaqx008 • 10
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