User: hjsunbio

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hjsunbio10
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Posts by hjsunbio

<prev • 9 results • page 1 of 1 • next >
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Comment: C: gene_bodyCoverage.py No usable output...why?
... I useed read_distribution.py implemented in RSeqQC with ensemble GTF file, similar question occured, the gtf2bed problems. Using differnt methods, I failed to transfer the GTF to BED formats the scripts can. A error occured every time. see below. Followed your instruction, I fixed the format problem ...
written 23 days ago by hjsunbio10
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Comment: C: Two parts of small intestine from same individuals, It's technical or biological
... Thanks a lot and sorry for the delay response. It is really a big hand for me. Actually, this is a big concern of one reviewer of our work. I have read all the materials you provided, below is my table for construct model matrix. I would like to know whether it is right. Another question is how shou ...
written 4 months ago by hjsunbio10
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Two parts of small intestine from same individuals, It's technical or biological replicates?
... **Background** We have an RNA-seq project on small intestine. The experimental design were like this: Four physiological states, each with three individuals (biological replicates), each individual with two samples (two parts of small intestine), thus 4 physiological states × three individuals × tw ...
rna-seq written 4 months ago by hjsunbio10 • updated 4 months ago by Asaf8.4k
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Comment: C: Continuous mismatch at the end of the alignment, how to eliminate it?
... Thank you for your answere. I do have used localpair mode, but the trailing unaligned regions were still there. mafft set as below. mafft --localpair --maxiterate 1000 --adjustdirectionaccurately ...
written 2.1 years ago by hjsunbio10
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Comment: C: Continuous mismatch at the end of the alignment, how to eliminate it?
... The alignments are now in fasta format. Sorry for delaying the reply, Since I am a newer here, I only can make five post in six hours, so I can't answer all question immediately. Could you help me with more details about using biopython or perl or awk to solve the problem. ...
written 2.1 years ago by hjsunbio10
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Comment: C: Continuous mismatch at the end of the alignment, how to eliminate it?
... Yes, they are probably different isoforms or assembly errors, what I want is to get the consensus part. ...
written 2.1 years ago by hjsunbio10
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Comment: C: Continuous mismatch at the end of the alignment, how to eliminate it?
... I need to deal with more than 6000 genes, so manual editing would be much time-consuming. ...
written 2.1 years ago by hjsunbio10
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Comment: C: Continuous mismatch at the end of the alignment, how to eliminate it?
... Thank you for your suggestion. ...
written 2.1 years ago by hjsunbio10
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Continuous mismatch at the end of the alignment, how to eliminate it?
... Since I am a newer here, I only can make five post in six hours, so I can't answer all question immediately. I just post the answer below 1. Q:There may be a method available in biopython to edit the variable part out. What format are the alignment files in at this time?@genomax A:The alignments ...
alignment sequence rna-seq written 2.1 years ago by hjsunbio10

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