User: Holly

gravatar for Holly
Holly30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
3 years, 8 months ago
Joined:
6 years, 10 months ago
Email:
m**************@epa.gov

Posts by Holly

<prev • 10 results • page 1 of 1 • next >
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Seq Qc/Trimming Code Preferences?
... Does anyone have any preferences that they might like to share regarding QC/Trimming tools for RNAseq? I have been testing FASTX, FASTQC and Prinseq. I like Prinseq the best so far, and also know there is alot available on bioconductor. I need sometihing that will feed into Bowtie/Tophat. Opinions? ...
qc trimming next-gen rna written 6.7 years ago by Holly30 • updated 6.6 years ago by Chris Penkett470
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Bowtie/Tophat With Fasta Converted From Fastq In Qc With Fastx ?
... I am looking at using FASTX to do some QC and trimming? Anyone familiar with that? Also, is it a problem to get fasta files recognized in Bowtie/Tophat? I have only come across fastq in the documentation. thanks, holly ...
tophat fastx bowtie written 6.7 years ago by Holly30 • updated 3.6 years ago by Biostar ♦♦ 20
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Changing Bowtie Settings In Tophat?
... Is anyone familiar with how Tophat is running Bowtie? I am assumiung the default paramerters, but can this be modified for improved alignment? or do people just twwek some of the many Tophat parameters? thanks. holly ...
tophat alignment bowtie written 6.8 years ago by Holly30 • updated 6.8 years ago by Chris Penkett470
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Comment: C: Tophat Error: No Such File Or Directory: 'S_1_Sequence.Fq'
... duh.. got it. thanks. on to the next error! Error: qual length (60) differs from seq length (35) for fastq record ! using two seq files from Pickrell for testing. ??? ...
written 6.9 years ago by Holly30
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Comment: C: Counting Repeat And Unique Reads Of Tophat Output
... do you know what the NM and XS specify? ...
written 6.9 years ago by Holly30
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Comment: C: Tophat Error: No Such File Or Directory: 'S_1_Sequence.Fq'
... can you tell me if y ou put your input sequence datafiles in the same directory? After moving my indexes to the index file as you suggested, I still get the 'no such file in directory' error. many thanks for your help. ...
written 6.9 years ago by Holly30
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Comment: C: Tophat Error: No Such File Or Directory: 'S_1_Sequence.Fq'
... thanks ! once I remove the H, I get the following error: Could not find Bowtie index files /wikihomedir/hmortens/human_test/hg18_c.* ...
written 6.9 years ago by Holly30
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Comment: C: Tophat Error: No Such File Or Directory: 'S_1_Sequence.Fq'
... i think this may be a memory error from what I see others experiencing. ...
written 6.9 years ago by Holly30
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Comment: C: Tophat Error: No Such File Or Directory: 'S_1_Sequence.Fq'
... I unpacked my reference index and two sequence files in my data folder 'human_test' command entered tophat -r 20 /wikihomedir/hmortens/Humantest/hg18c s1sequence.fq s2sequence.fq ...
written 6.9 years ago by Holly30
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Tophat Error: No Such File Or Directory: 'S_1_Sequence.Fq'
... new to tophat...any idea where the datafiles need to be for the program to recognize? The test files ran fine. thanks ...
tophat written 6.9 years ago by Holly30 • updated 3.2 years ago by Biostar ♦♦ 20

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