User: elisheva

gravatar for elisheva
elisheva70
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Location:
Israel
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5 days, 4 hours ago
Joined:
9 months, 1 week ago
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Posts by elisheva

<prev • 67 results • page 1 of 7 • next >
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Comment: C: Best way to generate a bed file
... Maybe I didn't understand your answer... what does it mean $10? Isn't it simply column 10? ...
written 14 days ago by elisheva70
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Comment: C: Best way to generate a bed file
... I edited my post, so you can see now.... And no, I have one Id per line and then all the exons coordinates ...
written 14 days ago by elisheva70
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Comment: C: Best way to generate a bed file
... Thanks! About your question: that's my data.... But I have one more problem - I just gave an example - the number of exons for each gene is different. ...
written 14 days ago by elisheva70
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Best way to generate a bed file
... Hello everyone! I have to do something and I kind of lost. I have 2 tab delimited text files which contains exons coordinates. the first fie contains the start coordinates (for example): NM_032291 chr1 + 66999638 67091529 67098752 67101626 NM_001308203 chr1 + 66999251 66999928 67 ...
exons bed file written 14 days ago by elisheva70 • updated 14 days ago by geek_y7.8k
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Comment: C: Help with finding introns
... I copied the transcripts to a new file and now it works. I have no idea why it didn't work before.... As for your question I created these urls using some commands - (as you wrote above) on cDNAs fasta file to extract the transcripts ids. It worked fine till this specific transcript ...
written 7 weeks ago by elisheva70
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Comment: C: Help with finding introns
... Sorry for all this mess, but now I see that the error was this: Traceback (most recent call last): File "introns.py", line 44, in main(line) File "introns.py", line 15, in main r.raise_for_status() File "/usr/lib/python2.7/dist-packages/requests/models.py", li ...
written 7 weeks ago by elisheva70
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Comment: C: Help with finding introns
... O.K. thanks. How can I ensure That it wont repet this error? After all I downloaded these transcripts from ensembl. So I don't get why the url is wrong. ...
written 7 weeks ago by elisheva70
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Comment: C: Help with finding introns
... Thank you so much!! I saw you wrote another solution But I allready used th first one.(Mainly because I use python 2.7) The problem is when I run this transcript: ENST00000537694.1 I get an error: Traceback (most recent call last): File "introns.py", line 44, in mai ...
written 7 weeks ago by elisheva70
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Comment: C: Help with finding introns
... Thanks so much!! I have one more question: What does it mean: "mask_feature"? And Is there is a short way to generate fasta file of all the introns: >transcript.index_of_intron sequence.... . ...
written 7 weeks ago by elisheva70
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Comment: C: Help with finding introns
... I'm only want the introns - preference to the second one. ...
written 7 weeks ago by elisheva70

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