User: miyagi

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miyagi0
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Posts by miyagi

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Comment: C: 10x Cell Ranger 'count' function error:
... I tend to agree, but what concerned me was the fact that it looks like this would have had to be done post-clustering to identify non-EC clusters, in which case it should be normalized before identifying those. So you think basically they took those cells out and then just provided the raw reads/n ...
written 8 days ago by miyagi0
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Comment: C: 10x Cell Ranger 'count' function error:
... Ok I see, I'm only now seeing that these are multiplexed reads. Unfortunately I haven't done de-multiplexing yet. I'll work on that... But if in the meantime anyone is able to tell me if there is anyway I could understand whether the processed file they deposited is normalized or not, i would reall ...
written 8 days ago by miyagi0
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Comment: C: 10x Cell Ranger 'count' function error:
... Thanks, The reason I did that is according to their file with explanations: https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-8077/E-MTAB-8077.sdrf.txt only the 8 files above are from brain. So I guess the other R1 files are from another tissue. ...
written 8 days ago by miyagi0
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Comment: C: 10x Cell Ranger 'count' function error:
... Hi at @genomax, Yes I actually started with those files, but they're problematic (or at least not clear). Long story short, it is not clear to me if these are normalized reads. These are definitely post-processed reads because they write in the paper that they 'excluded' cells that belong to non-e ...
written 8 days ago by miyagi0
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Comment: C: 10x Cell Ranger 'count' function error:
... Hi @swbarnes2, thanks for the reply! unfortunately changing the name to brain1_ATTCTAAG_S1_L001_R2_001.fastq.gz didn't work. Very frustrating... I doubt this is the case, but I noticed that the original file names have either L1/L5 (bolded) and all of the files are R2. 180908_I127_FCHWNVWBBXX_ ...
written 8 days ago by miyagi0
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10x Cell Ranger 'count' function error:
... Dear all, I am trying to use CellRanger 'count' function on the 10x single-cell data deposited here (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-8077/). I tried it two ways: **1) While in the directory where the fastq.gz files are:** cellranger count \ --id=Kalucka_endo \ ...
10x cellranger single cell written 9 days ago by miyagi0
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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 16 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 16 months ago by miyagi0 • updated 16 months ago by genomax85k
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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 16 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 16 months ago by miyagi0

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