User: lamia_203

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lamia_2030
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Posts by lamia_203

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Comment: C: Alignment loop using STAR
... I added this code and it worked overnight, thank you! Just to confirm, is this limiting the size of the BAM files? or is it doing something else? ...
written 4 days ago by lamia_2030
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Comment: C: Alignment loop using STAR
... Jan 10 19:59:01 ..... started sorting BAM EXITING because of FATAL ERROR: number of bytes expected from the BAM bin does not agree with the actual size on disk: 4944559 4928845 15 Jan 10 19:59:03 ...... FATAL ERROR, exiting EXITING because o ...
written 5 days ago by lamia_2030
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Comment: C: Alignment loop using STAR
... I had a slightly different code where the --runThreadN was set to 20 and it was aborting but now with it set to 10 its coming up with error message about not enough space for bam - however this time its continuing onto the next sample despite the error message ...
written 5 days ago by lamia_2030
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Alignment loop using STAR
... I'm running scRNA-seq and am trying to create a loop for all samples to run alignment. However, the loop stops about 20 or so samples later. Am I missing something from code? The alignment works fine without the loop. for i in *.fastq.gz do STAR --genomeDir ./human_index \ ...
alignment star rna-seq written 5 days ago by lamia_2030 • updated 5 days ago by swbarnes24.7k

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