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Recent Replies
Comment: using txt file to pass pathways for pipelines
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Hugo
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Thanks for the help Pierre, but it did not work.
I receive the same message for every iteration (just change the file pathway):
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- Python (Data analysis and machine learning)
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I think you're reading `?goana.DGELRT` rather than `?goana`. Type `methods(goana)` to see the methods available. The default method support…
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I assume that the differential results table is complete and contains all expressed genes rather than just the 12 genes shown in your post.…
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your bed file is actually a BEDPE file because you specified to use the -bedpe flag to `bedtools bamtobed`. it has two chr, start, and end …
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Did you test that? It still searches `.` so the entire `$(pwd)`, no?
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`?goana` indicates that the function needs `an DGELRT or DGEExact object`, so that you cannot easily rebuild (if at all) from that table. S…
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cat name_path3.txt | paste - - | while read entrada saida ; do muscle -in "${entrada}" -out "${saida}" ; done
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It is the name of the fastq.gz file. It is not part of the file. My apologies. it just pops up when I run the bash script in prompt.
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what i sthat altai5 in front of '@SQ' ?
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Dear Pierre,
Here is the answer to your questions (Iguess it works):
altai5@SQ SN:NC_036879.1 LN:224244399
@SQ SN:NC_…
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for what it's worth, "supplementary alignments" can be quite interesting. they often indicate things like SVs
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In that case use an aligner of your choice and extract reads that map: https://www.biostars.org/p/56246/#56251
Be sure to get primary alig…
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Yeah I was just trying to find the set of reads that were used to make up the final assembly. Some of those raw reads will definitely not a…
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