User: oars

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oars40
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Posts by oars

<prev • 32 results • page 1 of 4 • next >
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Sorting file by column, with missing values
... I'm trying to sort a file by max values in column 8 (Raw), here is a sample of the data: ![glimmer screen shoot][1] I tried to tackle this dataset with the following sort script: sort -t$'\t' -k8,8 -nr glm_ref.detail2 > glm_ref_detail_sort however, the output file keeps sorting on the fi ...
sort glimmer awk written 7 days ago by oars40
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Answer: A: grep errors for FASTA file (possible glimmer error?)
... I don't know what I did correct but I finally created the output file, even after producing the same errors??? ...
written 9 days ago by oars40
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Comment: C: grep errors for FASTA file
... Thanks - I did email the POC listed in the users manual so maybe he'll have some insight on what is going wrong. ...
written 9 days ago by oars40
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grep errors for FASTA file (possible glimmer error?)
... I am using the ‘extract’ program in glimmer to extract sequences for predicted genes. For some reason I keep getting an error with my grep step and cannot figure out why. My command is as follows: extract -2 assem31.fa glm_assem31.predict | grep -v X > glm_assem31.predict.seq And I get the ...
grep glimmer written 9 days ago by oars40
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Comment: C: New to Glimmer: trouble with .icm file
... I'm not sure what went wrong but I repeated my steps on my mac (I was using a linux machine before), and it worked. If anyone else that's new to glimmer has a similar issue, the **$ glimmer3 EC.fasta glm_ref.icm glm_ref** command should produce an .icm file in your directory of choice. If successf ...
written 11 days ago by oars40
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New to Glimmer: trouble with .icm file
... I'm brand new to glimmer and gene assembly and prediction. I'm having a hiccup with the "build the model" step. I write the following command: $ build-icm –r glm_ref.icm < glm_ref.long.seq At this point I think I'm on track. My understanding is the model information is saved to a binary f ...
gene prediction glimmer written 15 days ago by oars40
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Comment: C: FASTQ Phred33 average base quality score
... This worked, thank you. The output was 18.035 which I believe translates to at ASCII value of ~ 51. ...
written 23 days ago by oars40
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Comment: C: FASTQ Phred33 average base quality score
... Many thanks. Where you have | paste - - |, this is where I re-enter my file name? because as written I just return the following: > ...
written 23 days ago by oars40
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FASTQ Phred33 average base quality score
... I have a FASTQ dataset where I'm trying to find the average base quality score. I found this old link that helped somewhat (https://www.biostars.org/p/47751/). Here is my script (I'm trying to stick to awk, bioawk or python): bioawk -c fastx '{print ">"$name; print meanqual($qual)}' XXX.cl ...
fastq ascii phred33 written 23 days ago by oars40 • updated 23 days ago by WouterDeCoster26k
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Comment: C: Sequence Length Distribution From A Fastq File
... Thanks! This was a winner. ...
written 23 days ago by oars40

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