User: Lhl
Lhl • 730
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Posts by Lhl
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... Hi @va90,
I think you can do
```
pileupcolumn.get_query_sequences(mark_matches=True, mark_ends=True, add_indels=True)
```
This will reproduce mpileup format, from which you can infer all types of variants.
Another shortcut is to use `pileupread.indel`, it returns positive values incidcating inser ...
written 3 days ago by
Lhl • 730
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... The current intestiy values are transformed to intergers to save space of storage.
To transform them back to raw, you will need these digitisation, offset, and range values.
Have a look at
https://github.com/nanoporetech/fast5_research/blob/52a0b92e3bae0a6bbf3b61b2bde670c65827bfb0/fast5_research/f ...
written 18 days ago by
Lhl • 730
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... well done. xiao-ming ...
written 8 months ago by
Lhl • 730
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... Hi Folks,
I just found that with perl regex, I got variants frequencies that summed up to exceed sequencing depth.
cut -f5 test.pileup | perl -ne 'chomp; @del = $_ =~ /\-\d+[AGCTN]/ig; @ins= $_ =~ /\+\d+[AGCTN]/ig; @m = $_ =~ /\./g; print scalar (@del) ."\t". scalar (@ins). "\t". scalar (@m). " ...
written 8 months ago by
Lhl • 730
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... Hi ATpoint,
thanks for reminding me to post the commands.
Copy the string into a file -- String.txt
perl regex:
```
perl -ne 'chomp; @a = $_ =~ /\-\d+[AGCTN]/g; @b = $_ =~ /\+\d+[AGCTN]/g; print scalar (@a),"\t",scalar (@b),"\n";' String.txt
128 23
```
pysamstats commad:
```
pysamstats py ...
written 8 months ago by
Lhl • 730
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... Hi There ,
Have you ever compared the variants frequencies computed using pysam with that computed simply through perl regex?
I recently found some discrepensy between the two.
In the example below:
With perl regex, the number of deletions counted from pileup file is 128, but in the pysamstats re ...
written 8 months ago by
Lhl • 730
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... Have you sorted out? ...
written 3.2 years ago by
Lhl • 730
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... Hi Apelin20.
I am doing the same thing to orthomcl2.0 output -- groups.txt.
Have you, by any chance,, found any other way of processing the output for downstream analyses? ...
written 3.6 years ago by
Lhl • 730
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... I ran into the same error,
I wonder if you have solved the issue.
...
written 3.7 years ago by
Lhl • 730
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... Have you tried genBlastA/G ?
(She et al., 2011) genBlastG: using BLAST searches to build homologous gene models. Bioinformatics. ...
written 3.8 years ago by
Lhl • 730
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