Question: SAM file generation problem
0
gravatar for kuhelikadas1995
14 days ago by
kuhelikadas19950 wrote:

my SAM files generated are of 1.1kb each.. also the alignmnt is not done.. what to do??

rna-seq • 144 views
ADD COMMENTlink modified 14 days ago • written 14 days ago by kuhelikadas19950

Please put some more effort into your questions to get proper help.

  • What programs are you using?
  • Show us the complete commands you were using.
ADD REPLYlink written 14 days ago by finswimmer12k
nohup hisat2 --dta -cufflinks -x ../5.Reference_genome/genome -1 ../4.Trimmed_fastq/SRR1131659_Trimmed_1.fastq.gz -2 ../4.Trimmed_fastq/SRR1131659_Trimmed_2.fastq.gz -S SRR1131659.sam -p 20 &

this was the command used for aligning the adapter trimmed fastq files against human refernce genome. the SRA data here is paired end rna seq data. Command used for adapter trimming is:

cutadapt -a AGATCGGAAGA -A AGATCGGAAGA -o SRR1131659_Trimmed_1.fastq.gz -p SRR1131659_Trimmed_2.fastq.gz -m 20 SRR1131659_R1.fastq.gz SRR1131659_R2.fastq.gz -q 30
ADD REPLYlink modified 14 days ago by genomax70k • written 14 days ago by kuhelikadas19950
1

In the future when you paste code examples, highlight your code and click the "101 010" button to make it a code block, makes it easier to read.

Formatting options

ADD REPLYlink written 14 days ago by manuel.belmadani1.1k

done. but it didnot work. same problem. no alignmnt done.

ADD REPLYlink written 14 days ago by kuhelikadas19950

If it did not work then why did you accept the answer below?

ADD REPLYlink written 14 days ago by genomax70k

I accepted the answer nd tried.. then saw that i didnt work..

ADD REPLYlink written 14 days ago by kuhelikadas19950

Can show us the file sizes for your original and trimmed data, as well as your genome? One thing I notice is that in your cutadapt command, the quality filter (-q 30) is after the input files whereas in the documentation it's typically before.

If your trimmed files are suspiciously small I would guess that's the error.

ADD REPLYlink modified 14 days ago • written 14 days ago by manuel.belmadani1.1k

raw data for r1 read is of size 502.3MB and that of r2 is of 498.8MB.. trimmed data for r1 is of 489.6MB and that of r2 is 486.6MB.. moreover, applying

-q 30before or after made no difference. Size of reference genome is 1.1GB(zipped file) and 4.5GB(when unzipped)

ADD REPLYlink modified 14 days ago • written 14 days ago by kuhelikadas19950
1

As I recall HISAT2 is one of those programs that is sensitive to order of program options and input files. So you may want to pay some attention to that order. Did you generate the indexes yourself and are they known to work?

ADD REPLYlink modified 13 days ago • written 13 days ago by genomax70k

yeah.. and it did generate the indexes for genome by myself.. nothing was mentioned about the adapteer sequence.. it used AGATCGGAAGA.. for both forward and reverse end reads. should i use AGATCGGAAGAGC as the adapter sequence fr both the end reads??

ADD REPLYlink modified 13 days ago • written 13 days ago by kuhelikadas19950

Specifying an incorrect adapter sequence should have no impact on being able to produce a good SAM file from HISAT2. It sounds like that is where your problem lies. Have you looked at the log file for HISAT2 to see if there are any errors that can be addressed?

ADD REPLYlink modified 13 days ago • written 13 days ago by genomax70k

initially i had used the command

cutadapt -a AGATCGGAAGA....and so on I mean i skipped the "-A adapter2" part keeping rest of the command same , initially for trimming.. but that command is for single end data..whereas my data is of paired end..That time SAM files generated were of 4.4GB each or more ..and BAM files were of around 1.2GB each. but problems started showing up (SAM files are being generated of 1.1kb each..and BAM files stop being executed after 800 bytes or so) when i used the cutadapt command mentioning both adapters 1 and 2;(the cutadapt command shown in the very 1st comment of mine)as shown below:

> cutadapt -a AGATCGGAAGA -A AGATCGGAAGA -o SRR1131659_Trimmed_1.fastq.gz -p SRR1131659_Trimmed_2.fastq.gz -m 20 SRR1131659_R1.fastq.gz SRR1131659_R2.fastq.gz -q 30
ADD REPLYlink modified 13 days ago • written 13 days ago by kuhelikadas19950
1
gravatar for manuel.belmadani
14 days ago by
Canada
manuel.belmadani1.1k wrote:

Change --dta -cufflinks to --dta-cufflinks.

ADD COMMENTlink written 14 days ago by manuel.belmadani1.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1666 users visited in the last hour