tag:blogger.com,1999:blog-5967565047811298492.post5512062231232102058..comments2024-03-26T03:36:01.677-07:00Comments on All About Bioinformatics: Converting Cufflinks .GTF predictions to .BED filesAnonymoushttp://www.blogger.com/profile/15813086589943781474noreply@blogger.comBlogger9125tag:blogger.com,1999:blog-5967565047811298492.post-20983127750638207712019-05-13T10:50:12.372-07:002019-05-13T10:50:12.372-07:00Bondi Two Seat Sofa Beach. Store Price: $1,550.00....Bondi Two Seat Sofa Beach. Store Price: $1,550.00. Black Rice Price: $850.00. Picture of Bondi Three Seat Sofa Beach. Bondi Three Seat Sofa Beach. <a href="https://mrhomeappliances.com/seven-best-folding-beds-for-your-house" rel="nofollow">queen size rollaway beds</a>Mr Bob Billshttps://www.blogger.com/profile/04066348437312227950noreply@blogger.comtag:blogger.com,1999:blog-5967565047811298492.post-39110235292507069082018-05-14T10:05:00.197-07:002018-05-14T10:05:00.197-07:00Hi, I tried the script, it works well with plus st...Hi, I tried the script, it works well with plus strand ("+"), however for minus strand ("-"), it does not seem to give right result, result in negative numbersAnonymoushttps://www.blogger.com/profile/13122477480227128145noreply@blogger.comtag:blogger.com,1999:blog-5967565047811298492.post-81834908105745564382017-01-03T12:44:20.825-08:002017-01-03T12:44:20.825-08:00Hi, thanks for the script.
I am using gtf output ...Hi, thanks for the script. <br />I am using gtf output from StringTie tool. When I ran the script it warns that 'Warning: no FPKM field'<br /><br />The FPKM value on field[8] is different from cufflinks<br />e.g <br />gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "transcript:Sb01g000200.1"; ref_gene_id "gene:Sb01g000200"; cov "0.064565"; FPKM "0.019950"; TPM "0.026536";<br />gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "transcript:Sb01g000200.1"; ref_gene_id "gene:Sb01g000200"; cov "0.064565";<br /><br />How do I alter the code to catch the FPKM value the current regular expression syntax is not working.<br /><br />Thanks<br />Anonymoushttps://www.blogger.com/profile/01370917143419544157noreply@blogger.comtag:blogger.com,1999:blog-5967565047811298492.post-57462225944297492552016-12-24T20:29:34.289-08:002016-12-24T20:29:34.289-08:00Use redirection (">"). See the follow...Use redirection (">"). See the following link: http://linuxcommand.org/lts0060.php Anonymoushttps://www.blogger.com/profile/15813086589943781474noreply@blogger.comtag:blogger.com,1999:blog-5967565047811298492.post-6361287847239169632016-12-23T21:03:22.779-08:002016-12-23T21:03:22.779-08:00Hi, Thanks for this great script. However, I don&#...Hi, Thanks for this great script. However, I don't know how to save the output. When I run the script to convert my gtf file, everything was outputted to my screen rather than saving a file. What should I do? Thanks in advance!Anonymoushttps://www.blogger.com/profile/10277385873519037315noreply@blogger.comtag:blogger.com,1999:blog-5967565047811298492.post-80774746745672309542015-09-17T02:34:32.936-07:002015-09-17T02:34:32.936-07:00This comment has been removed by the author.historypakhttps://www.blogger.com/profile/12429820414620086221noreply@blogger.comtag:blogger.com,1999:blog-5967565047811298492.post-13770048046541418292012-02-08T16:52:46.264-08:002012-02-08T16:52:46.264-08:00This is due to the different syntax between python...This is due to the different syntax between python 2.7 and python 3. I wrote this script for python 3, so it will cause problems if you use python 2.7.Anonymoushttps://www.blogger.com/profile/15813086589943781474noreply@blogger.comtag:blogger.com,1999:blog-5967565047811298492.post-76713133901396034782011-12-09T07:52:45.008-08:002011-12-09T07:52:45.008-08:00This comment has been removed by the author.Gireesh Kumar Boguhttps://www.blogger.com/profile/00480928522385944082noreply@blogger.comtag:blogger.com,1999:blog-5967565047811298492.post-4174032260967757782011-12-09T07:50:05.717-08:002011-12-09T07:50:05.717-08:00Greatscript. However I got this error
gisnb111:dat...Greatscript. However I got this error<br />gisnb111:datasets bogugk$ python gtf2bed.py cufflinks-TranscriptDeNovo.gtf <br /><br /> File "gtf2bed.py", line 36<br /> print('Warning: no gene_id field ',file=sys.stderr);<br /> ^<br />SyntaxError: invalid syntaxGireesh Kumar Boguhttps://www.blogger.com/profile/00480928522385944082noreply@blogger.com