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Old 05-22-2015, 12:34 AM   #17
kaps
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Location: Uganda

Join Date: Jan 2015
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Quote:
Originally Posted by Michael.Ante View Post
Hi Kaps,

you should have a look at the Bowtie2 homepage. There, it is explained in detail how the programs work. At the end of the manual is a "Lambda phage example", which has quite an overlap to your problem. It also has a SAMtools downstream section...

Cheers,
Michael
I have used a reference (comprising of 2 sequences varying in length) to do alignment on paired end fastq files. I have generated the sam file but when i try converting it (sam) to bam, it is not working!
here is the feedback: samtools view -bS 4_S4_paired.sam 4_S4_paired.bam
[main_samview] random alignment retrieval only works for indexed BAM or CRAM files.
▒BC▒m▒▒N▒0D▒ܜK▒X=p[▒qU|
▒ ▒▒▒5r[SY▒I▒▒▒O▒sH[@▒▒▒f▒▒▒a0▒w3▒Rʄq▒▒G▒[▒2▒▒Q▒Lk▒֋▒ vU▒1)J▒ei▒M&"▒qq5▒Q^ݒ▒▒▒▒▒`▒ U▒▒▒Q▒ vI▒▒▒f▒▒q▒▒:;▒=▒▒P▒▒U▒▒"n\o3▒ε▒
▒;*(n▒J)*▒▒▒▒֙%▒zM19H▒I▒▒▒▒▒5{▒>▒S▒H▒Qt▒~▒▒▒
▒▒y▒▒

when with -bT, I get a similar feedback as;
samtools view -bT cp4genome.fa 4_S4_paired.sam 4_S4_paired.bam
[samfaipath] build FASTA index...
[fai_build_core] different line length in sequence '4_S4_contig_23'.
[samfaipath] fail to build FASTA index.
[main_samview] random alignment retrieval only works for indexed BAM or CRAM files.
▒BC▒m▒▒N▒0D▒ܜK▒X=p[▒qU|
▒ ▒▒▒5r[SY▒I▒▒▒O▒sH[@▒▒▒f▒▒▒a0▒w3▒Rʄq▒▒G▒[▒2▒▒Q▒Lk▒֋▒ vU▒1)J▒ei▒M&"▒qq5▒Q^ݒ▒▒▒▒▒`▒ U▒▒▒Q▒ vI▒▒▒f▒▒q▒▒:;▒=▒▒P▒▒U▒▒"n\o3▒ε▒
▒;*(n▒J)*▒▒▒▒֙%▒zM19H▒I▒▒▒▒▒5{▒>▒S▒H▒Qt▒~▒▒▒
where is the problem?
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