User: michael.ante

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michael.ante3.5k
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Posts by michael.ante

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Comment: C: Using featureCount with a GFF file
... Your SEQ-ID in the example gff lines is 003__g__Streptococcus_no_23 *Prodigal:2.6*; that I wanted to know. Using featureCounts, the names and choordinates from your gff and the alignment have to be identical. Here it seems that your alignment is on transcriptome level, while your gff is on genomi ...
written 9 days ago by michael.ante3.5k
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Comment: C: Using featureCount with a GFF file
... Are the chromosome names identical? Does the alignment contain the "Prodigal..." in the names? Since you did DNA-Seq, I'd try to get a samtools idxstat report first, to get an idea where the alignments are located. ...
written 10 days ago by michael.ante3.5k
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Comment: C: Bedtools problem : It looks as though you have less than 3 columns at line: 1.
... Hi Tomm, Check your bed file with `sed -n 'l'` there you'll see all control characters. Was the original file made in Windows? If so try `dos2unix`. Cheers, Michael ...
written 23 days ago by michael.ante3.5k
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Comment: C: salmon was only able to assign 0 fragments to transcripts
... Building a suffix array for the human transcriptome in 0.0001873s and the whole index within 0.0052422s would make me suspicious even on a dedicated workstation. ...
written 27 days ago by michael.ante3.5k
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Comment: C: awk, copy and paste single line command
... From the most inner steps (the `sed '1d' penicillin_SNPs.txt | cut -d "_" -f 2 ` and `sed '1d' penicillin_SNPs.txt | cut -f 4` ) . Looking at your code: you have `<(paste <(sed ...) <(sed ..) | awk '{}') ` should the awk command not be used after the paste output? ...
written 28 days ago by michael.ante3.5k
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Answer: C: awk, copy and paste single line command
... Edit ( https://www.biostars.org/u/41557/ ): scroll down to see answer by OP -------------------- --- In one cut call, you use "_" as delim char, in the other you don't. If you get errors like this, dissect your one-liner in the single steps. Try first, what your `sed .. | cut` steps result in , ...
written 28 days ago by michael.ante3.5k • updated 3 days ago by Kevin Blighe51k
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Comment: C: bbduk flags 'tossbrokenreads' and 'nullifybrokenquality'
... You have the read ID, check in each step if this asynchronous base/quality ratio appeared. Try to find the read in the original sra file. Check with a simple script if this is the only case. If it was introduced in one of your steps, try to reproduce the error. If the error is reproducible, contact ...
written 4 weeks ago by michael.ante3.5k
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Comment: A: bbduk flags 'tossbrokenreads' and 'nullifybrokenquality'
... How did you perform 'decontamination'? The error is clearly, that the base-string's length differs from its associated quality-string length. Personally, I would rather investigate the problem than trying to solve it by bbmap. ...
written 4 weeks ago by michael.ante3.5k
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Answer: A: Interpret genome alignment results
... Hi, Little changes on nucleotide level can lead to drastic changes on protein level. In a worst case scenario, you might introduce a frame shift with a mutation in a gene's 5' region which lead to a totally different products. You'll have in such a case nearly 100%identity on nucleotide level but n ...
written 4 weeks ago by michael.ante3.5k
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Comment: C: Are reads with the same length and position always "duplicates"
... Is this RNA-Seq or DNA-Seq? In case of RNA, is it whole transcritome, targeted, or 3' seq? Please find a good explanation why you see duplications [here][1]. Without proper molecular indexes, it's hard distinguishing between gene expression caused overrepresentation and PCR duplicates. For PCR ...
written 4 weeks ago by michael.ante3.5k

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