User: getanid123

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getanid1230
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Posts by getanid123

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Batch estimate using kBET
... I have done kBET batch correction for three single cell RNA seq batches consisting of 15, 15 and 20 cells each. Studying gene expression of knock out and wild type mouse and the single cell RNA technology used is SMARTseq2. I have given the input matrix with columns as samples [50] and rows as genes ...
batch correction kbet written 7 months ago by getanid1230
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Comment: C: Why does abyss not produce contig files when I run in a loop on server
... Hi john, Yes the output files were saved on a different directory. The system has 512GB and 16GB RAM. The output file [.dot, .fa, .hist, .path, .path.dot ] are generated but I kind of deleted them to go for a new run [which generated all the data I needed]. But would appreciate if you can guide me a ...
written 9 months ago by getanid1230
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Comment: C: Why does abyss not produce contig files when I run in a loop on server
... It is a big task if I have to check all the samples for contigs.fa and regenerate all the missing contigs. I just wanted to know if I need to specify -np or -j parameters. I want to assign specific processes or threads to be on safe side. ...
written 9 months ago by getanid1230
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Comment: C: Why does abyss not produce contig files when I run in a loop on server
... I was looking in particular for scaffolds and contigs files and they are not generated. But I was able to generate these files after running it again using same command line [outside loop]. ...
written 9 months ago by getanid1230
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Why does abyss not produce contig files when I run in a loop on server
... Hi all, I was trying to run abyss 2.2.4 and I came across an issue. The loop includes running 5 kmers on 20 samples. The code used is as follows: abyss-pe name='name' k='kmervalue' in = 'file1_r1.fq file1_r2.fq' My loop is running fine and execute all 100 samples. But for 5 samples in betwee ...
de novo assembly abyss written 9 months ago by getanid1230 • updated 9 months ago by lieven.sterck9.0k
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Comment: C: single cell RNA seq batch correction question
... Thank you so much!! ...
written 9 months ago by getanid1230
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Comment: C: single cell RNA seq batch correction question
... Thank you so much jared.andrews07!! The data is in fastq format and obtained from SMARTseq platform. As per your suggestion I will be doing QC-> alignment -> batch correction -> differential expression analysis -> dimensionality reduction/clustering Can you please confirm if the abo ...
written 9 months ago by getanid1230
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single cell RNA seq batch correction question
... Hi All, I am a newbie in computing biological data and I have 30 samples ranging from 3-8GB size obtained when studying embryonic development of cells in small and large groups.I was doing batch correction as first step of my pipeline and was struck with this step. I am planning to do kBET and MNNc ...
rna-seq written 9 months ago by getanid1230

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