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Search: Posts Made By: vadim
Forum: General 02-22-2013, 06:46 AM
Replies: 7
Views: 1,621
Posted By vadim
If the data mentioned in the articles is public...

If the data mentioned in the articles is public but not in the archive. Maybe the authors did not have enough time/resources to submit the data to SRA.
Forum: General 02-22-2013, 06:18 AM
Replies: 7
Views: 1,621
Posted By vadim
I know this may sound weird, but have you...

I know this may sound weird, but have you considered submitting their data?

Btw, could you share the articles please?
Forum: General 07-19-2012, 12:37 AM
Replies: 1
Views: 753
Posted By vadim
samtools index <bam file> samtools view <bam...

samtools index <bam file>
samtools view <bam file> chr1:115251042-115251155
Forum: Bioinformatics 06-15-2012, 06:57 AM
Replies: 13
Views: 5,086
Posted By vadim
The spot descriptor claims that the read length...

The spot descriptor claims that the read length is 150bp, 75 forward and 75 reverse. But the actual read length is 100 bases only. I guess fastq-dump just obeys the rules by splitting the read at 75,...
Forum: Bioinformatics 06-15-2012, 05:43 AM
Replies: 13
Views: 5,086
Posted By vadim
Could you post the run accession please?

Could you post the run accession please?
Forum: Bioinformatics 03-09-2012, 01:19 AM
Replies: 6
Views: 2,066
Posted By vadim
I am the developer of CRAM and can answer any...

I am the developer of CRAM and can answer any questions about it.

The code is here:
https://github.com/vadimzalunin/crammer/

Documentation can be found here: ...
Forum: De novo discovery 02-22-2012, 12:33 AM
Replies: 36
Views: 21,345
Posted By vadim
The link is broken.

The link is broken.
Forum: Bioinformatics 01-20-2012, 02:01 AM
Replies: 15
Views: 8,909
Posted By vadim
I believe SRR123456.fastq contains the...

I believe SRR123456.fastq contains the "leftovers": reads with missing mates (due to filtering etc. )
Forum: Bioinformatics 12-05-2011, 12:53 AM
Replies: 15
Views: 4,813
Posted By vadim
Could you please provide an example?

Could you please provide an example?
Forum: Bioinformatics 11-17-2011, 03:14 AM
Replies: 15
Views: 4,813
Posted By vadim
SRA* accessions are NCBI submission accessions,...

SRA* accessions are NCBI submission accessions, similarly ERA* accessions are EBI submission accessions and DRA* are DDBJ submission accessions.
Sometimes study is submitted before the run data,...
Forum: Bioinformatics 11-17-2011, 02:11 AM
Replies: 15
Views: 4,813
Posted By vadim
What do you mean by SRA id? Each SRA run should...

What do you mean by SRA id? Each SRA run should be associated with a study through SRA experiment. The XML schema might be useful:
http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-3/
or...
Forum: Bioinformatics 11-17-2011, 01:36 AM
Replies: 15
Views: 4,813
Posted By vadim
Grab the full XML dump and parse it: ...

Grab the full XML dump and parse it:
ftp://ftp-trace.ncbi.nlm.nih.gov/sra/reports/Metadata/NCBI_SRA_Metadata_Full_20111101.tar.gz
Forum: Bioinformatics 07-19-2011, 03:04 AM
Replies: 1
Views: 714
Posted By vadim
Have you tried adding '2>somefile' to the command...

Have you tried adding '2>somefile' to the command line?
Forum: Illumina/Solexa 07-19-2011, 03:02 AM
Replies: 2
Views: 954
Posted By vadim
http://www.ddbj.nig.ac.jp/ ...

http://www.ddbj.nig.ac.jp/
http://www.ebi.ac.uk/ena/
http://www.ncbi.nlm.nih.gov/sra
Forum: Bioinformatics 07-18-2011, 12:53 AM
Replies: 6
Views: 2,309
Posted By vadim
Given that tophat works fine from command line I...

Given that tophat works fine from command line I assumed that bowtie is already in $PATH. Therefore something could be wrong with tophat itself, for example it is not in $PATH. But you are right,...
Forum: Bioinformatics 07-15-2011, 03:06 AM
Replies: 3
Views: 1,132
Posted By vadim
Have you tried 'sfffile -i'?

Have you tried 'sfffile -i'?
Forum: Bioinformatics 07-15-2011, 12:19 AM
Replies: 6
Views: 2,309
Posted By vadim
Does it work with absolute path then?

Does it work with absolute path then?
Forum: Bioinformatics 07-14-2011, 07:14 AM
Replies: 6
Views: 2,309
Posted By vadim
Do you read output and error streams of the...

Do you read output and error streams of the process? Probably the buffers are just full.
Forum: Bioinformatics 07-06-2011, 12:50 AM
Replies: 1
Views: 821
Posted By vadim
The line does not look like a valid SAM record to...

The line does not look like a valid SAM record to me - many fields are missing, for example bases and quality scores. Are all records in the file like that?
Forum: General 07-06-2011, 12:32 AM
Replies: 2
Views: 1,488
Posted By vadim
Is it possible that you are using BAM as input? ...

Is it possible that you are using BAM as input?
If both input and output are text SAM format, could you do 'head -3' on both of them and post here?
Forum: Bioinformatics 06-30-2011, 07:56 AM
Replies: 41
Views: 14,462
Posted By vadim
You may also want to do this prior to sorting: ...

You may also want to do this prior to sorting:
export LC_ALL=POSIX
Forum: Bioinformatics 06-30-2011, 07:04 AM
Replies: 41
Views: 14,462
Posted By vadim
Could you try sorting with this command? sort...

Could you try sorting with this command?
sort -s -k 1,1 my_file.sam > my_file.sorted.sam

This will sort by the first column only, ignoring everything else.
Forum: Bioinformatics 06-30-2011, 03:57 AM
Replies: 41
Views: 14,462
Posted By vadim
Have you actually tried this? cat...

Have you actually tried this?
cat my_file.sorted.sam | sort -s -c -k 1,1

Another thought is that in your example reads are not sorted by mate order, that is the second mate in the pair comes...
Forum: Bioinformatics 06-30-2011, 02:21 AM
Replies: 41
Views: 14,462
Posted By vadim
Does HTSeq expect reads to be sorted by name? In...

Does HTSeq expect reads to be sorted by name? In which case the sort order should be easy to check:
cat my_file.sorted.sam | sort -s -c -k 1,1
Forum: Bioinformatics 06-21-2011, 01:00 AM
Replies: 18
Views: 4,219
Posted By vadim
It should work under windows, see here: ...

It should work under windows, see here:
http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

It is not licensed, I asked them recently about it and they said "no restrictions",...
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