User: alexadeanfitz

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Posts by alexadeanfitz

<prev • 11 results • page 1 of 2 • next >
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Comment: C: AfterQC Cannot Find Output
... Thank you, the underscore was the issue ...
written 15 months ago by alexadeanfitz10
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AfterQC Cannot Find Output
... I have run AfterQC using python2.7 on a folder containing fastq files, I get no errors in the terminal window however I cannot locate the generated output folders and it runs too fast for me to think it actually worked, any advice? Lab-iMac:lab$ cd /Users/Alexa/Alexa/SRP135669/fastq/fastq ...
rna-seq afterqc written 15 months ago by alexadeanfitz10 • updated 15 months ago by genomax75k
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bwa mem cannot locate output bam file
... Hello, Below is the script I ran, first I indexed the reference fasta file, then I ran BWA-MEM and I cannot locate the output aln.bam file User$ /Users/Alexa/Alexa/SRP135669/fastq/bwa index -a is -p PAO1_index /Users/Alexa/Alexa/SRP135669/fastq/PAO1_index.fasta [bwa_index] Pack FASTA... ...
bwa mem rna-seq written 15 months ago by alexadeanfitz10 • updated 15 months ago by ATpoint26k
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Comment: A: Preprocessing for DESeq2 - create metadata table
... I believe that 1,10 means I want the sampleNO to be divided based on the first 10 characters in the fastq file? ...
written 15 months ago by alexadeanfitz10
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Comment: C: Preprocessing for DESeq2 - create metadata table
... Ignore first question - caused by me cut and pasting script from text editor, the quotation symbols were different ...
written 15 months ago by alexadeanfitz10
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Preprocessing for DESeq2 - create metadata table
... Hello, I have count tables from htseq-count and would like to run differential expression analysis using DESeq2 My understanding is that I need to also create an associated metadata table. I have 6 fastq files (2 from baseline condition, 2 from condition A and 2 from condition B). I am planning on ...
htseq-count deseq2 rna-seq written 15 months ago by alexadeanfitz10 • updated 15 months ago by h.mon28k
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Answer: A: htseq-count error utf-8 codec can't decode
... Error resolved for anyone having the same issue: I had downloaded the gff3 file from Ensembl bacteria and converted it to gtf using Galaxy. I did this because at first on Ensembl when I searched the reference genome I wanted, I did not see an option for a gtf file however I was able to go back to ...
written 15 months ago by alexadeanfitz10
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Comment: C: htseq-count error utf-8 codec can't decode
... I am using python 3.6 ...
written 15 months ago by alexadeanfitz10
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Comment: C: htseq-count error utf-8 codec can't decode
... I used linecache to print that line (8700), as well as the line just before to see if it is reading the file correctly however I only get a " symbol >>> import linecache >>>linecache.getline("/Users/Alexa/Alexa/SRP062593_sra/SRP062593_htseq/PA14_reference_NC_2.gtf", 8700) ...
written 15 months ago by alexadeanfitz10 • updated 15 months ago by Devon Ryan93k
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htseq-count error utf-8 codec can't decode
... Hello, I am trying to run htseq-count on bam files against a reference bacterial genome in gtf format, downloaded from Ensembl The RNA-Seq reads were single-end fastq files, I performed BWA-MEM using Galaxy which generated the bam files. I ran flagstat and got a high percentage of mapped reads, an ...
htseq-count rna-seq written 15 months ago by alexadeanfitz10

Latest awards to alexadeanfitz

Scholar 15 months ago, created an answer that has been accepted. For A: htseq-count error utf-8 codec can't decode

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