User: getanid123

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getanid1230
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Posts by getanid123

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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 3 days 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 3 days 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 4 days ago by getanid1230 • updated 3 days ago by lieven.sterck6.9k
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Comment: C: single cell RNA seq batch correction question
... Thank you so much!! ...
written 5 days 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 5 days 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 6 days ago by getanid1230

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