tag:blogger.com,1999:blog-4376119613549496246.post6173058417376563799..comments2024-03-27T23:36:17.389-07:00Comments on Diving into Genetics and Genomics: quality control of your fastq file! my first post after I got my PhD!tommyhttp://www.blogger.com/profile/04023008941349107659noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-4376119613549496246.post-72064103323595398542020-05-14T08:42:22.436-07:002020-05-14T08:42:22.436-07:00That will surely help you to transfer your one fil...That will surely help you to transfer your one file into another like those;<br /><br /><a href="https://simplefileconverter.blogspot.com/2020/04/how-to-convert-vob-file-to-mp4-file.html" rel="nofollow">Vob to Mp4</a><br /><br /><a href="https://simplefileconverter.blogspot.com/2020/04/how-to-convert-mov-file-to-flv-file.html" rel="nofollow">Mov to Flv</a><br /><br /><a href="https://simplefileconverter.blogspot.com/2020/04/how-to-convert-mpg-file-to-avi-file.html" rel="nofollow">Mpg to Avi</a><br /><br /><a href="https://simplefileconverter.blogspot.com/2020/04/how-to-convert-mxf-file-to-mov-file.html" rel="nofollow">Mxf to Mov</a><br /><br /><a href="https://simplefileconverter.blogspot.com/2020/04/how-to-convert-mpg-file-to-avi-file_26.html" rel="nofollow">Mpg to Avi</a><br /><br /><a href="https://simplefileconverter.blogspot.com/2020/04/how-to-convert-mid-file-to-wav-file.html" rel="nofollow">Mid to Wav</a>Fonts Maniahttps://www.blogger.com/profile/18406244480702938446noreply@blogger.comtag:blogger.com,1999:blog-4376119613549496246.post-65667423925294849032020-05-14T08:41:41.319-07:002020-05-14T08:41:41.319-07:00Hey Friends, Use this online converter for your f...Hey Friends, Use this online converter for your file converting;<br /><br /><a href="https://simplefileconverter.blogspot.com" rel="nofollow">Simple File Converter</a>Fonts Maniahttps://www.blogger.com/profile/18406244480702938446noreply@blogger.comtag:blogger.com,1999:blog-4376119613549496246.post-18396756091858379082014-08-05T07:28:50.190-07:002014-08-05T07:28:50.190-07:00my email: tangming2005@gmail.commy email: tangming2005@gmail.comtommyhttps://www.blogger.com/profile/04023008941349107659noreply@blogger.comtag:blogger.com,1999:blog-4376119613549496246.post-46501869338120851992014-08-03T06:39:41.370-07:002014-08-03T06:39:41.370-07:00I could not attach files, so send it on your email...I could not attach files, so send it on your email. CNhttps://www.blogger.com/profile/16662377337824094350noreply@blogger.comtag:blogger.com,1999:blog-4376119613549496246.post-23464892153098824282014-08-03T05:53:49.081-07:002014-08-03T05:53:49.081-07:00Can u please show the output of the over presented...Can u please show the output of the over presented sequences?tommyhttps://www.blogger.com/profile/04023008941349107659noreply@blogger.comtag:blogger.com,1999:blog-4376119613549496246.post-81032046676051466082014-08-02T00:30:52.223-07:002014-08-02T00:30:52.223-07:00Hi Tang,
I downloaded ribosome profiling raw read...Hi Tang,<br /><br />I downloaded ribosome profiling raw reads from <br />http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34743<br />For eg (this library) GSM854438<br /><br />FastQC check shows a lot of adapters<br />Then i used trimmomatic to trim the adapters. The adapter i used is the default adapter sequences from trimmomatic with the command:<br /><br />java -jar ~/unixTools/Trimmomatic-0.32/trimmomatic-0.32.jar SE fastQ/Ribosomal_WildType_2hpf_R1.fastq trimmed_Ribosomal_WildType_2hpf_R1_V2.fastq ILLUMINACLIP:adapterTrueSeq_2.fa:3:20:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:27<br />TrimmomaticSE: Started with arguments: fastQ/2hpf_R1.fastq trimmed_2hpf_R1_V2.fastq ILLUMINACLIP:adapterTrueSeq_2.fa:3:20:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:27<br /><br />Around 6% of sequences is gone.<br /><br />Check with FastQC again.<br />There is still a lot of adapter left. Then i used the adapters from your post. Then rerun the scripts.<br />Now only about 7% of the sequences are retained.<br /><br />Any insight on how to solve this would be highly appreciated. Thanks in advance !<br /> CNhttps://www.blogger.com/profile/16662377337824094350noreply@blogger.com