User: Lhl

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Lhl730
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Posts by Lhl

<prev • 115 results • page 1 of 12 • next >
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Comment: A: How to get inserted bases using pysam pileup
... 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 Lhl730
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Answer: A: what do digitisation, offset, and range values mean in fast5 file of Nanopore se
... 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 Lhl730
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Comment: C: How To Split A Bam File By Chromosome
... well done. xiao-ming ...
written 8 months ago by Lhl730
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demystify pileup format -- how to properly filter pileup format
... 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). " ...
next-gen alignment snp sequencing written 8 months ago by Lhl730
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Comment: C: pysamstats produces 'inaccurate' variants frequencies?
... 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 Lhl730
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pysamstats produces 'inaccurate' variants frequencies?
... 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 ...
snp written 8 months ago by Lhl730
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Answer: A: Should I Fix Branch Length In Paml Analyses?
... Have you sorted out? ...
written 3.2 years ago by Lhl730
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Comment: C: OrthoMCL: How to parse groups.txt for a phylogeny?
... 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 Lhl730
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Answer: A: MCScanX Error - Can't plot the graphs (Downstream analysis)
... I ran into the same error, I wonder if you have solved the issue. ...
written 3.7 years ago by Lhl730
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Answer: A: How To Concatenate Blast Results (M8) Via Setting Threshold Of Distance Between
... 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 Lhl730

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