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Forum: Bioinformatics 07-05-2015, 10:57 PM
Replies: 0
Views: 1,824
Posted By Tally
Picard MergeSamFiles: 'RG ID on SAMRecord not found in header' yet BAM has headers

Hi all,

I have a whole genome mammalian sample that was sequenced on 2 lanes of Illumina Hiseq.

I have aligned the paired fastq with BWA mem and sorted with SAMtools.

I merged the 2 BAM...
Forum: Bioinformatics 06-20-2012, 10:26 PM
Replies: 1
Views: 2,588
Posted By Tally
Illumina DNA sequence specific strand bias involving orphan reads

I have whole-genome DNA paired-end sequence from the Illumina HiSeq2000. I aligned this to the reference genome with BWA v.5.9 using the default parameters for paired-end.

I have detected an...
Forum: Bioinformatics 02-20-2012, 03:46 PM
Replies: 4
Views: 2,219
Posted By Tally
T is 7, forward A/G is 33, reverse A/G is 81, C...

T is 7, forward A/G is 33, reverse A/G is 81, C is 0

I don't think there is any way of knowing how many G's and A's from DP4, because these are both lumped under 'non-reference'. Have a look at...
Forum: Bioinformatics 02-20-2012, 03:38 PM
Replies: 8
Views: 16,424
Posted By Tally
DP4 refers to the reads covering the reference...

DP4 refers to the reads covering the reference forward, reference reverse, alternate forward, alternate reverse bases. Eg DP4=2,3,0,0 means 2 reads are the reference base, forward strand, 3 reference...
Forum: Bioinformatics 02-20-2012, 03:33 PM
Replies: 0
Views: 1,691
Posted By Tally
No reference/alternate (DP4) read depth in VCF?

Hi all,

I have produced a vcf file of aligned sequence data using samtools mpileup, with the -D flag set.

For some reason certain lines lack the "DP4=" information, eg:
...
Forum: Bioinformatics 01-23-2012, 01:57 PM
Replies: 20
Views: 19,070
Posted By Tally
When importing sam to bam, I use 'view' rather...

When importing sam to bam, I use 'view' rather than 'import' :

@SQ header lines present in SAM file:
samtools view –bS alignment.sam > alignment.bam

@SQ header lines absent from SAM file:...
Forum: Bioinformatics 11-27-2011, 04:07 PM
Replies: 5
Views: 3,907
Posted By Tally
Thanks for the responses, that is very helpful....

Thanks for the responses, that is very helpful. That certainly makes sense to give unmapped mates the mapped mate coordinates for sorting purposes, however it is confusing that BWA sets other fields...
Forum: Bioinformatics 11-24-2011, 03:36 PM
Replies: 5
Views: 3,907
Posted By Tally
Question BWA samflag inconsistencies

Dear bioinformatics community,

I have used BWA to align paired-end reads to a mammalian genome. I extracted orphan reads from the alignment with this command:

awk 'and ($2, 0x0004) && ! and...
Forum: Bioinformatics 10-17-2011, 07:48 PM
Replies: 1
Views: 1,578
Posted By Tally
I have a similar issue. My output log reports...

I have a similar issue. My output log reports n_reads*2 because they are paired end, but it looks like that is not the case for your data. My issue is the "x out of n raw reads are mapped" part:
...
Forum: Bioinformatics 09-29-2011, 04:12 PM
Replies: 5
Views: 4,761
Posted By Tally
I'm not sure about your pileup issue, but see the...

I'm not sure about your pileup issue, but see the thread "samtools tview reference sequence" regarding the string of N's in your tview. For me, this was caused by having a colon character in the...
Forum: Bioinformatics 09-29-2011, 12:16 AM
Replies: 20
Views: 19,070
Posted By Tally
Thank you VeBeKay!! That solved my problem...

Thank you VeBeKay!! That solved my problem perfectly :-) However I had to delete it in the reference AND rerun the alignment and subsequent steps, time-consuming but 100% effective.
I am surprised...
Forum: Bioinformatics 09-05-2011, 08:48 PM
Replies: 3
Views: 8,683
Posted By Tally
Dear Rodrigo, Yes you are correct. The blue...

Dear Rodrigo,
Yes you are correct. The blue means quality of 0-9 and so on for the other colours. Higher scores mean higher qualities.
You were also correct with the orphan reads: These are reads...
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