Bioconductor,
  I am working on an RNA sequencing experiment on Arabidopsis (Illumina,
100bp, single end), using tophat to map the reads, and R for the rest.
 Many (9 of 12) libraries worked with out error.  Three of the libraries
had no `accepted_hit.bam` file, while they did have a junctions.bed, and
had an error of "Error: could not convert to BAM with samtools".  in the
standard error output.

Additionally in tophat_out/log/accepted_hits_sam_to_bam.log
[samopen] SAM header is present: 7 sequences.
Parse error at line 19971338: CIGAR and sequence length are inconsistent

Obviously, somewhere the CIGAR  or sequence lengths were altered and no
longer 'mesh'.
I run :

library(ShortRead)
reads <- readFastq("myFile")
treads <- trimEnds(reads, a = "5")     #trim at a quality score of 20
nreads <- treads[width(reads) > 21]    # keep only reads longer than 21 bp
writeFastq(nreads, "myNewFile.fastq")

then a 'normal' (few options changed) tophat call
tophat -p 4 -o outdir -G my.gtf         BowtieIndex        myNewFile.fastq

Any ideas on what went wrong, and why it didn't work some of the time?
 Should I just rerun the trimming scripts and see if they map afterwards?


Thanks in advance!

> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] ShortRead_1.18.0     latticeExtra_0.6-24  RColorBrewer_1.0-5
[4] Rsamtools_1.12.3     lattice_0.20-15      Biostrings_2.28.0
[7] GenomicRanges_1.12.3 IRanges_1.18.1       BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] Biobase_2.20.0 bitops_1.0-5   grid_3.0.0     hwriter_1.3
 stats4_3.0.0
[6] zlibbioc_1.6.0

-- 
Sam McInturf

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