User: lqdo2000

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lqdo200020
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Australia
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Posts by lqdo2000

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Comment: C: How to retrieve the sample origin of contigs after assembly of pooled reads?
... Is there a way/metric to assess the similarity between 2 datasets (here transcriptomes)?  ...
written 4.4 years ago by lqdo200020
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Comment: C: How to retrieve the sample origin of contigs after assembly of pooled reads?
... Yes, I also tried by removing the exact duplicate sequences in the contig dataset. But some unique sample A and sample B contigs could be similar. So, what you mean is that the contigs (or at least the read/contig matching regions) are not different enough for segregating them precisely? What about ...
written 4.4 years ago by lqdo200020
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How to retrieve the sample origin of contigs after assembly of pooled reads?
... I have 2 different samples for which I sequenced the transcriptomes (Illumina): sample A and sample B. I pooled all the single-end reads (up to 300 bp) from the 2 samples together and did a de novo assembly with CLC. Now I am trying to retrieve from which sample the contigs (up to 3,000 bp) come f ...
reads assembly alignment contigs written 4.4 years ago by lqdo200020 • updated 4.3 years ago by Biostar ♦♦ 20
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Comment: C: Incompatibility between BioPython SeqIO module and pymol?
... Sorry, for seq_record_seq it was a typo (corrected). The stout doesn't return any error (same when I use the other syntax: pymol.cmd.do("save %s.pdb, all" % seq_record.id)). But when I use this syntax, it returns that the number of selected atoms is either "0" or lower then the total sequence. ...
written 5.0 years ago by lqdo200020
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Incompatibility between BioPython SeqIO module and pymol?
... Hi, I am trying to generate .pdb files from fasta sequences using BioPython SeqIO module to parse them to Pymol, and fab command: from Bio import SeqIO for seq_record in SeqIO.parse(file, "fasta"):   pymol.cmd.do("fab %s, %s" % (seq_record.seq, seq_record.id)) pymol.cmd.save("%s.pdb" % seq_ ...
python pymol biopython written 5.0 years ago by lqdo200020 • updated 4.8 years ago by Biostar ♦♦ 20
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Comment: C: ImportError: No module named pymol (Mac)
... Fixed ! I exported the path to the parent folder of the one containing _cmd.so to PYTHONPATH in my ~/.bash_profile. Works like a charm ! Thanks a lot João for your help ! ...
written 5.0 years ago by lqdo200020
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Answer: A: ImportError: No module named pymol (Mac)
... Hi João, Thanks for your help ! I followed your advice and installed PyMOL and all the dependencies with MacPort (it installed it in /opt/local/bin/pymol). I also linked pymol binary to /Library/Python2.7/site-packages. But still the same error (i.e. ImportError: no module named pymol). I am clear ...
written 5.0 years ago by lqdo200020
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ImportError: No module named pymol (Mac)
... Hi,   Being new to python scripting, I am facing a simple problem. I am writing a python script "MyScript.py" in which I am calling the third-part program PyMOL through the import function. Here is the simplified script (mainly inspired from this blog: http://doeidoei.wordpress.com/2009/02/11/py ...
python pymol written 5.0 years ago by lqdo200020
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Comment: C: How To Interpret The Flagstat Output After Mapping Reads Back To Contigs Of A De
... Alright, I see. Thank you very much for your help Istvan ! ...
written 5.8 years ago by lqdo200020
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Comment: C: How To Interpret The Flagstat Output After Mapping Reads Back To Contigs Of A De
... Thanks Istvan ! Ok, I didn't know for KmerGenie. I tried VevetK and VelvetOptimizer but they returned a value of 1 ! Is there anything else I could try to estimate the best k length? Yes, data are strand specific (sequenced with MiSeq). I assumed the read R1 set referred to forward and the read R2 ...
written 5.8 years ago by lqdo200020 • updated 5.8 years ago by Istvan Albert ♦♦ 81k

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