User: miyagi

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miyagi0
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Posts by miyagi

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Comment: C: Changing FASTQ format from sense to antisense
... Thanks for the formatting tip. The issue is that I'm using their Bluebee Analysis Pipeline (https://www.lexogen.com/lexogen-and-bluebee-launch-slamdunk-data-analysis-pipeline/) and so the error in this picture ![enter image description here][1] is totally useless unfortunately. I realize it is proba ...
written 8 months ago by miyagi0
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Changing FASTQ format from sense to antisense
... Dear all, I am trying to analyze some RNA-seq results from a method called SLAM-seq. Long story short, their recommended library prep is Quantseq whereas we used Kappa Poly-A. We figured out after sequencing that the difference between these includes using different strands for first strand synthe ...
rna-seq written 8 months ago by miyagi0 • updated 8 months ago by genomax73k
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Comment: C: fastx_reverse_complement truncating files?
... Hey, thank you! haha .I know.. you'd think this very simple thing would work. The worst part is not even getting a proper error. I understand what you're saying about the wc -l, though that would not explain the difference in size of the files right (0.976 GB vs 1.15). I'll give seqtk a shot and upd ...
written 8 months ago by miyagi0
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Comment: C: fastx_reverse_complement truncating files?
... and i'm getting an error indicating the file is corrupted when using a downstream software analysis ...
written 8 months ago by miyagi0
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Comment: C: fastx_reverse_complement truncating files?
... regardless, the GB of the files goes from being 1.15 for the original file to 0.976 to the new file even though both are compressed ...
written 8 months ago by miyagi0
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Comment: C: fastx_reverse_complement truncating files?
... I just use $ wc -l input.fastq.gz and compare that to $ wc -l output.fastq.gz ...
written 8 months ago by miyagi0
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Comment: A: fastx_reverse_complement truncating files?
... hi thanks for the reply, the input file is a fastq, however i'm comparing the length to the original fastq.gz file because i know that the fastq file and the compressed file will have different lengths. ...
written 8 months ago by miyagi0
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fastx_reverse_complement truncating files?
... Dear all, I am using FASTX-Toolkit 0.0.14-foss-2016a and using the command line: $ module load FASTX-Toolkit; fastx_reverse_complement -z -i [input.fastq] -o [output.fastq.gz] When I use: $ wc -l input.fastq.gz I get 6191703 returned vs. 4742402 for the length of the output.fastq. ...
reverse compliment fastx rna-seq written 8 months ago by miyagi0 • updated 8 months ago by ATpoint24k

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