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Sequence alignment with biopython

sequence alignment written 2 hours ago by alec_djinn • 330 • updated 12 minutes ago by Bastien Hervé ♦ 3.9k

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how to interpret hisat2 result

assembly alignment rna-seq written 3 hours ago by fatimarasool135 • 20 • updated 3 hours ago by WouterDeCoster ♦ 38k

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142

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GATK HaplotypeCaller Problems

software error gatk next-gen alignment written 4 weeks ago by chengye • 10 • updated 12 hours ago by Biostar ♦♦ 20

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Job: Senior Scientist Programmer, Spiral Genetics, Seattle, WA

genome assembly next-gen job alignment written 14 hours ago by niranjan • 0

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ClustalO computing suboptimal alignment

alignment clustalomega written 18 hours ago by mschmid • 90

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Error in RNA editing tool sprint

software error alignment rna-seq written 25 days ago by hirahameed222 • 0 • updated 16 hours ago by cchmczhang • 0

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Alignment of short sequences allowing gaps and wildcards

gaps short-sequences alignment dna wildcards written 21 hours ago by filippo.martignano • 10

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Domain Prediction Tools for Windows

alignment written 22 hours ago by Chat-ra • 20

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Recent Replies

C: Fold change cut off enrichment analysis by eshansharma15 • 20
Arbitrary cut-offs can be misleading, therefore one also needs joined neighboring intervals in su...
C: some unrelated info in SAM file generated by BWA by Bastien Hervé ♦ 3.9k
I have this one `Version: 0.7.17-r1188` -o FILE sam file to output results to [stdout]
A: Sequence alignment with biopython by Bastien Hervé ♦ 3.9k
You can increase the gap penalty values, open and extend ones alignment = pairwise2.align.gl...
C: some unrelated info in SAM file generated by BWA by zhangdengwei • 10
Sorry, my version of BWA is 0.7.12-r1039, and there is no *-o* option. Did we use the same version?
C: TALL (acute lymphoblastic leukaemia) TCGA data vs other Cancers by Kevin Blighe ♦ 41k
Please read through to here: https://www.biostars.org/p/375737/
A: survival curve for a specific gene in T-cell acute lymphoblastic leukaemia by Kevin Blighe ♦ 41k
TARGET studied ALL, so, they may have some of the T-cell sub-types, which I believe are rare. HER...
C: Is it possible to convert .CHP files to .CEL? by shawn.w.foley • 400
Did you ever get a solution to this issues? I've just inherited some old projects with CHP files ...
C: Fold change cut off enrichment analysis by shawn.w.foley • 400
So it sounds like you're concerned about losing true signal by looking at too large a group of ge...
C: NIPT for microdeletion and microduplication sydnromes by Sej Modha ♦ 4.1k
Please read through the web page, there is a section for: #### NIPT for microdeletion and micro...
C: Segmentation fault (core dumped) in SOAP by Kevin Blighe ♦ 41k
Segmentation faults typically relate to memory / RAM, and may occur for diverse reasons. Develope...
C: NIPT for microdeletion and microduplication sydnromes by David_emir • 320
Thanks a lot for your quick response. You mentioned about RAPIDr ... My question still remains va...
C: fast-dump of 10x genomics SRA data by genomax ♦ 65k
That is correct. You could try to rewrite the headers in file 2 programmatically to match file 1 ...

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