User: chris.mit7

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chris.mit760
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Location:
United States
Last seen:
5 months, 1 week ago
Joined:
5 years, 7 months ago
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Posts by chris.mit7

<prev • 4 results • page 1 of 1 • next >
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Answer: A: Species-Specific Output From Blast -Db Nt -Remote ...
... Add -entrez_query "Homo Sapiens[Organism]" to your search or whatever organism you want. Such as: blastn -remote -db nr -query stuff_to_search.fasta -entrez_query "Homo Sapiens[Organism]" -evalue 1e-20 -num_alignments 10 > stuff_to_search.blastn ...
written 3.2 years ago by chris.mit760
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Tutorial: Reorder Vcf Files
... Here's a quick bash script to reorder a vcf file. It's currently setup to reorder a vcf to karotypic ordering. I've seen enough threads and have been annoyed at this myself enough times so hopefully someone else finds this useful. grep -P "^#" $1 > ${1}.header for i in {1..22} do grep -P ...
vcf tutorial written 4.5 years ago by chris.mit760 • updated 4.5 years ago by Isaac Turner50
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Comment: C: Strand Specific Tophat Output
... Have you looked at your FPKM distribution from the gtf files themselves? How about your alignment %? What sort of pre-processing did you do? ...
written 4.6 years ago by chris.mit760
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Answer: A: Selecting Random Pairs From Fastq?
... Bit old, but here's my solution import random f = open('CD4CD45RO_GATCAG_s_1_1_sequence.txt') f2 = open('CD4CD45RO_GATCAG_s_1_2_sequence.txt') o = open(f.name+'.sample', 'wb') o2 = open(f2.name+'.sample', 'wb') row = f.readline() sampleSize = 1000000 tSize = 66000000 f2pos = [] p = float(sampleSiz ...
written 5.6 years ago by chris.mit760

Latest awards to chris.mit7

Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Species-Specific Output From Blast -Db Nt -Remote ...
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Reorder Vcf Files

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