An assembly of reads, contigs and scaffolds

A blog on all things newbler and beyond

Posts Tagged ‘454AlignmentInfo.tsv’

Running newbler: de novo transcriptome assembly II: the output files

Posted by lexnederbragt on September 21, 2010

This post describes the transcriptome specific output files, or differencers between the files for transcriptome assembly relative to a regular assembly. For (aspects of) files not treated in this post have a look at these previous posts.

Alternative rope splicing (source: Wikimedia commons)

1) 454NewblerMetrics.txt
The differences for this file, relative to the same file for a ‘normal’ assembly (described in this post), are metrics on the isogroups and isotigs:

isogroupMetrics
{
numberOfIsogroups     = #####;
avgContigCnt          = #.#;
largestContigCnt      = ####;
numberWithOneContig   = #####;

avgIsotigCnt          = #.#;
largestIsotigCnt      = ##;
numberWithOneIsotig   = #####;
}

Besides the number of isogroups, the average and maximum number of contigs per isogroup are listed, as well as number of isogroups with only one contig. Below that, the average and maximum number of isotigs per isogroup are listed, as well as number of isogroups with one isotig. Read the rest of this entry »

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Newbler output VI: the ‘status’ files (454TrimStatus.txt, 454ReadStatus.txt, 454PairStatus.txt) and the 454AlignmentInfo.tsv file

Posted by lexnederbragt on May 20, 2010

The files that are the topic of this post are all tables, i.e. tab separated text files. The ‘status’ files describe what happened with all the reads and the paired end halves, while the AlignmentInfo file summarizes the contig alignments.

The fact that these files are tabular makes for easy parsing using by perl/python or, my favorite, awk.

1) 454TrimStatus.txt

Accno   Trimpoints Used Used Trimmed Length     Orig Trimpoints Orig Trimmed Length     Raw Length
ERGMJHS01CYVHW  5-78    74      5-98    94      100
ERGMJHS01D6IHL  5-116   112     5-116   112     161
ERGMJHS01DYTX5  5-127   123     5-127   123     173
ERGMJHS01DYDH0  5-78    74      5-78    74      124
ERGMJHS01ECEGM  5-256   252     5-256   252     271
ERGMJHS01CRQ8D  5-272   268     5-272   268     273
ERGMJHS01ECMVT  5-260   256     5-260   256     270
ERGMJHS01EZ7VU  5-41    37      5-61    57      62
ERGMJHS01ERDXB  5-207   203     5-207   203     252

This file describes what (trimmed) part of the read was considered for alignment. The columns describe:

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