User: lrutter

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lrutter0
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Posts by lrutter

<prev • 14 results • page 1 of 2 • next >
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Comment: A: Running SnpEff on Galaxy
... I see... Thank you for your explanation, Jennifer. ...
written 3.0 years ago by lrutter0
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Running SnpEff on Galaxy
... Hello, I would like to annotate a .vcf file and also summarize possible effects variants can have on genes (stop codon, amino acid changes, etc.) It seems that is what the output of SnpEff can provide (http://snpeff.sourceforge.net/SnpEff.html). I have uploaded a .vcf file, .fasta file, and .gff3 ...
galaxy snp written 3.0 years ago by lrutter0
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Comment: C: htseq-count obtains zero counts
... Jennifer: Thanks for your help, and thanks for sending calmness my way via Hiram! :o) Your suggestion did not work, but I think I found the problem. I was working with RNA-seq, and one of my classmates said BWA is better for DNA. When I tried using bowtie with -c option (for colorspace), there wer ...
written 3.6 years ago by lrutter0
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Comment: C: htseq-count obtains zero counts
... Wow, it is like music to my ears to hear that I might not have to remap... because I am rushing, unfortunately this time. It sounds like the first option you provided may be faster to get the count tables? (Next time, I would like to better understand what I am doing, and will read over your many he ...
written 3.6 years ago by lrutter0
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Comment: C: htseq-count obtains zero counts
... When I do a head on the SAM file used to generate the BAM file used in the "SAM/BAM Alignment Summary Metrics", I get the following (where the first line contains the characters that caused the bolded exception in my comment right above): @SQ    SN:AF001540    LN:1781 @SQ    SN:AF001541    LN:1138 ...
written 3.6 years ago by lrutter0
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Comment: C: htseq-count obtains zero counts
... Below is the output "log" of the SAM/BAM Alignment Summary Metrics on a BAM file (I bolded a line that does not look too good):   INFO:root:## executing java -Xmx4g  -Djava.io.tmpdir='/galaxy/main/scratch'  -jar /galaxy/main/deps/picard/1.56.0/devteam/picard/e0232cbac965/jars/CreateSequenceDiction ...
written 3.6 years ago by lrutter0
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Comment: C: htseq-count obtains zero counts
... Jennifer: Thank you. Your explanation explains what I have been puzzling over! I am not experienced, and did not know how to check the alignment, I just assumed it was okay. I ran "flagstat" on one of my BAM files, and it gave me an 11-line output: 6263972 + 0 in total (QC-passed reads + QC-faile ...
written 3.6 years ago by lrutter0
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htseq-count obtains zero counts
... I am using the following command: htseq-count -s no -a 0 FourA.sam hg19.gtf > FourA.count and getting zero counts in the output. I have tried -s as yes/no (I am almost sure it should be "yes" based off the site I got my files), and -a between 0 and 10. No matter what parameters, I get zero coun ...
htseq-count deseq2 rna-seq count written 3.6 years ago by lrutter0 • updated 3.6 years ago by Jennifer Hillman Jackson23k
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Comment: C: BWA for SOLiD
... It looks like it went through the "BWA for SOLiD" and created a SAM file! I have five more of these files, though. We'll see if they all go through. Thanks again for your help, Jen! ...
written 3.6 years ago by lrutter0
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Comment: C: BWA for SOLiD
... I just submitted the "BWA for SOLiD". I am not sure how long it is approximated to take? But I will update. Thanks again :o) ...
written 3.6 years ago by lrutter0

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