Tag: IOError

Help with error velocyto

Help with error velocyto 0 Hi Biostars, I try to get the loom file and after trying I still don’t know how to fix this error: velocyto run -b MT/outs/filtered_feature_bc_matrix/barcodes.tsv -o output_dir -m Hg38_rmsk.gtf MT/outs/possorted_genome_bam.bam /cellranger/reference/refdata-cellranger-GRCh38 -3.0.0/genes/genes.gtf –samtools-memory 8000 –samtools-threads 8 MemoryError: bam file #0 could not be sorted by…

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Errors while trying to run Scenic

Errors while trying to run Scenic 0 Hello, I have been trying to runScenic2 but I keep getting the error below: runSCENIC_2_createRegulons(scenic2, coexMethod=c(“top5perTarget”))# Toy run settings 17:06 Step 2. Identifying regulons [1] “IOError: Failed to open local file ‘/Users/sp2037/Desktop//NA’. Detail: [errno 2] No such file or directory” Error in runSCENIC_2_createRegulons(scenic2,…

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Use kaggle kernel inside kaggle notebook

I want to use this command !kaggle kernels output iliasparalikas/dcgan -p . to download the outputs of the previous notebook to this one so i can continue training.It works fine in my local machine, but when I try to use it i get this error Traceback (most recent call last):…

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bcl2fastq error with RunInfo.xml

bcl2fastq error with RunInfo.xml 0 Dear all, I am running to an error with bcl2fastq. I have slightly different setup – I have received ONLY two files from the sequencing company in order to run conversion. One of the files is in tar.gz.dm5 which contains a single line: daac12b61f03f01d303f7b47f9118994 220202_VH00203_129_AAANKJFM5.tar.gz…

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How to do Binding and Expression Target Analysis?

How to do Binding and Expression Target Analysis? 0 Hello I used BETA to infer direct target genes from ChIP-seq peaks. Can someone help to let me know what is wrong with the program? I can not get feedback from GitHub. Is there a similar tool that can do the…

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How to write out a ID and AA sequence from a SWISS PROT database file into a new file in a specific order using python?

I have a Swiss-Prot database file that contains several Swiss-Prot Files. They are copied and pasted underneath each other. Therefore there is one Swiss-Prot entry after another listed in the same file. I want to write the ID into another file as the header. Immediately underneath, I want to write…

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IOError [errno 2] No such file or directory: ‘-o’

TopHat error: IOError [errno 2] No such file or directory: ‘-o’ 2 Hello everyone. I’m now running tophat in our server. First, I just simply tried “tophat -p 8 -G <gtf_file> <ref_genome> <fa1><fa2>” and it worked. Then I wrote a for loop scripts but It reported error: [2019-04-03 10:49:16] Beginning…

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