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I sent only a part of my email (Samuele Gherardi) 3. tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi XLOC_000001 - - MT-ND5 - chr M:0-16571 12484.2 12260.8 12707.7 11447 11233.1 11661 XLOC_000002 - - USP14 TSS1, TSS2, TSS3 chr8586-236453 16.7235 9.41244 24.0346 19.437 11.7368 27.1371 XLOC_000003 - - SMCHD1 TSS10, TSS11, TSS12, TSS4, TSS5, TSS6, TSS7, TSS8, TSS9 chr19322-2728540 28.2493 17.5093 38.9892 27.2263 16.6263 37.8262 XLOC_000004 - - EMILIN2 TSS13, TSS14 chr80607-2882469 3.98118 0 7.99721 4.62875 0.278519 8.97899 I this is normal, how can I find the class code of transcript listed in the Cuff Diff gene expression file? Message: 2 Date: Thu, 0000 To: "[email protected]" Content-Type: text/plain; charset="iso-8859-1" Hello everybody, I'm quite new in NGS world, I'm trying to analize dome RNA-seq data.

Re: Downloadable Galaxy Virtual Machine in VMware (Nate Coraor) 7. (Johnson, Kory (NIH/NINDS) [C]) Message: 1 Date: Thu, 0000 To: "[email protected]" Content-Type: text/plain; charset="iso-8859-1" this is an example of my Cuff Diff gene fpkm tracking file.

With kind regards, Jan Message: 6 Date: Thu, -0500 To: "Haarst, Jan van" Content-Type: text/plain; charset=iso-8859-1 This is great!

I haven't checked the image out, but I'm fetching the torrent now and will leave it seeding here from PSU to help out.

The idea is that better quality scores indicate the base is reliably reported, while poor quality scores reflect uncertaintly about the true identity of the base.

These files represent the primary data generated by the sequencer, and will be requested by other researchers after you publish your study. If you are using Life Tech/ABI Solid sequencers, the data may be returned as a color space FASTQ file (usually with a *.csfastq" extension) The most important thing you can do once you get primary data off the sequencer is back to it up.

Most modern sequencers produce FASTQ files as output, which is a modified version of a traditional FASTA formatted file.

FASTQ flles are ASCII text files that encode both nucleotide calls as well as 'quality information', which provides information about the confidence of each nucleotide.

Such that, a user can look at the discordance rates via box plot as you would/can for quality scores observed across all reads, and pick a refined criteria for filtering. If you have received this electronic information in error, please notify the sender immediately by telephone. To: Johnson, Kory (NIH/NINDS) [C]; [email protected]: Re: [galaxy-user] FASTQ collapse? what if 2 have an identical sum, but different strings (which is probably not uncommon)?

a similar scenario I could imagine sometimes being useful would be 'collapse sequences, but don't count Ns as mismatches'.

certainly possible, but more complicated than simply collapsing reads that are 100% sequence-identical. Assaf or someone from galaxy could perhaps answer better.

all of these are possible, but it starts becoming less transparent and more complex.

collapsing FASTQ to FASTA is simply a way to remove that problem.


  1. Provided on a best effort basis - and may go out of date! Links to useful resources Bullet XFEL data. as cluster status and file system problems. Users can self-subscribe here https//de/sympa/info/maxwell-user. FastX graphics connections available using a FastX client. In an emergency, there is also a web.

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  3. Notably in the above output the paired-end information was lost when the data was extracted from the NCBI SRA using fastq-dump with default settings. Further to note, with newer fastq-dump the extracted sequences have double-length and it turns out fastq-dump concatenates sequence of the forward and reverse reads.

  4. I dont have any intimate knowledge here, but my guess is that it comes down to defining what quality scores to keep. collapsing sequences is easy. the sequences either they match or they dont. handling sequence+quality is harder. would you keep the quality string with the highest total sum of qualities? what if 2 have an.

  5. May 19, 2015. Open-source command-line utilities for bioinformatics such as the EMBOSS package Rice et al. 2000, the FASTX tools Gordon, 2009 or the scripts that come with BioPerl Stajich et al. 2002 typically. For the most recent and up to date information, please follow the links in the main text of the article.

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