User: antonioggsousa

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Posts by antonioggsousa

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Comment: C: problem with setting up uniprot database for Diamond BLAST
... So, that is your problem. You are not getting any fasta files without `DNA` or `additional`. If you search in the subfolders (at least below 2 subfolders) of the `uniprot` folder do you see `fasta.gz` files without `DNA` or `additional` in their names? It seems to me that you have from the print, ...
written 3 days ago by antonioggsousa1.9k
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Comment: C: problem with setting up uniprot database for Diamond BLAST
... Do the following command: `find . -mindepth 2 | grep "fasta.gz" | grep -v 'DNA' | grep -v 'additional' | wc -l` This will tell if you are finding any files to `cat` next and how many files. ...
written 3 days ago by antonioggsousa1.9k
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Comment: C: problem with setting up uniprot database for Diamond BLAST
... Did you run these commands successfully before: > mkdir -p uniprot > wget -q -O uniprot/reference_proteomes.tar.gz \ ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/$(curl \ -vs ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/ref ...
written 3 days ago by antonioggsousa1.9k
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Comment: C: Qualimap: java.lang.RuntimeException: The raw data doesn't exist for sample ?
... The separator between both columns is a tab? Did you try with and without the `-r` option? ...
written 4 days ago by antonioggsousa1.9k
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Answer: C: Qualimap: java.lang.RuntimeException: The raw data doesn't exist for sample ?
... Not sure if it is related with copy/paste, but the file `target.interval_list` does not have any file extension. Is this file a GFF/GTF or BED file? Regarding the file `bam_file.txt`, the first column, I think it is the sample name that you want to give, not necessarily the same as the file name. ...
written 4 days ago by antonioggsousa1.9k
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Comment: C: fastqc output analysis
... Hi, Without showing the plots it is difficult to comment. I would say that (depending also on the library prep) it is normal to have a warning/error (orange/read) flags on **Per base sequence content**, specially a bias in the beginning that depends on the library prep, as well as **Sequence Dupli ...
written 4 days ago by antonioggsousa1.9k
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Comment: C: Using STAR to map fastq files: EXITING: because of fatal INPUT ERROR: number of
... Make sure that the file name is correct as well as the path. ...
written 4 days ago by antonioggsousa1.9k
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Comment: C: Using STAR to map fastq files: EXITING: because of fatal INPUT ERROR: number of
... Now it looks Ok with the exception of a lack of space between `Day-30-R3_S1_L008_R2_001.fastq--outSAMattrRGline` the fastq sample and the parameter. After these corrections, are you still getting the same error? ...
written 4 days ago by antonioggsousa1.9k
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Comment: C: Using STAR to map fastq files: EXITING: because of fatal INPUT ERROR: number of
... If you want to provide a list of SE fastq files you need to provide this list separated by comma and not space, such as: > --readFilesIn file_1.fastq,file_2.fastq,file_3.fastq If you have PE fastq give two lists separated by comma and for the forward and reverse fastq files with a space betwee ...
written 4 days ago by antonioggsousa1.9k
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Comment: C: picard sortsam error
... Sorry for the late reply. Just to tell you that both commands finished. The `awk` command did not throw nothing to `stdout`. The `ValidateSamFile` threw the following last messages: INFO 2021-01-09 01:28:58 SamFileValidator Validated Read 640,000,000 records. Elapsed time: ...
written 5 days ago by antonioggsousa1.9k

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